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ESP: PubMed Auto Bibliography 18 Feb 2025 at 01:52 Created:
Microbial Ecology
Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.
Created with PubMed® Query: ( "microbial ecology" ) NOT pmcbook NOT ispreviousversion
Citations The Papers (from PubMed®)
RevDate: 2025-02-17
Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] [Epub ahead of print].
Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.
Additional Links: PMID-39961999
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@article {pmid39961999,
year = {2025},
author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM},
title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39961999},
issn = {1678-4405},
support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; },
abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.},
}
RevDate: 2025-02-17
Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.
Marine environmental research, 205:107017 pii:S0141-1136(25)00074-1 [Epub ahead of print].
As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.
Additional Links: PMID-39961275
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@article {pmid39961275,
year = {2025},
author = {Wang, A and Bong, CW and Tao, S and Ye, X and Liu, B and Liang, H and Zheng, X and Wong, YY and Loh, KH and Li, H and Chen, K and Lim, SH and Lee, CW},
title = {Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.},
journal = {Marine environmental research},
volume = {205},
number = {},
pages = {107017},
doi = {10.1016/j.marenvres.2025.107017},
pmid = {39961275},
issn = {1879-0291},
abstract = {As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.},
}
RevDate: 2025-02-17
Microbial ecology of Serpentinite-hosted ecosystems.
The ISME journal pii:8019724 [Epub ahead of print].
Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.
Additional Links: PMID-39961017
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@article {pmid39961017,
year = {2025},
author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES},
title = {Microbial ecology of Serpentinite-hosted ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.
Microbial ecology, 88(1):6.
Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.
Additional Links: PMID-39960660
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@article {pmid39960660,
year = {2025},
author = {Gomi, R and Adachi, F},
title = {Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {6},
pmid = {39960660},
issn = {1432-184X},
support = {JP22K18038//JSPS KAKENHI/ ; 22B006//Kurita Water and Environment Foundation, Japan/ ; 2230113//Sumitomo Foundation, Japan/ ; JPMEERF20235R01//Environment Research and Technology Development Fund/ ; },
mesh = {*Escherichia coli/genetics/drug effects ; *Quinolones/pharmacology ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Genomics ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.},
}
MeSH Terms:
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*Escherichia coli/genetics/drug effects
*Quinolones/pharmacology
*Escherichia coli Proteins/genetics
*Anti-Bacterial Agents/pharmacology
*Plasmids/genetics
Genomics
Drug Resistance, Bacterial/genetics
Genome, Bacterial
RevDate: 2025-02-15
CmpDate: 2025-02-15
Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.
Microbial ecology, 88(1):5.
Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.
Additional Links: PMID-39954056
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@article {pmid39954056,
year = {2025},
author = {Ren, Z and Gao, H and Martyniuk, N and Ren, H and Xiong, X and Luo, W},
title = {Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {5},
pmid = {39954056},
issn = {1432-184X},
support = {2023YFF1303700//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/isolation & purification/genetics ; China ; *Rivers/microbiology ; Biodiversity ; Ecosystem ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.},
}
MeSH Terms:
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*Soil Microbiology
*Ice Cover/microbiology
*Bacteria/classification/isolation & purification/genetics
China
*Rivers/microbiology
Biodiversity
Ecosystem
Soil/chemistry
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
RevDate: 2025-02-15
Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.
Biosensors & bioelectronics, 276:117232 pii:S0956-5663(25)00106-X [Epub ahead of print].
The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.
Additional Links: PMID-39954521
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@article {pmid39954521,
year = {2025},
author = {Hernández-Villamor, D and Li, P and Aydogan, M and Verhelst, M and Van de Wiele, T and Rabaey, K and Prévoteau, A},
title = {Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.},
journal = {Biosensors & bioelectronics},
volume = {276},
number = {},
pages = {117232},
doi = {10.1016/j.bios.2025.117232},
pmid = {39954521},
issn = {1873-4235},
abstract = {The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.},
}
RevDate: 2025-02-15
Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.
Journal of hazardous materials, 489:137608 pii:S0304-3894(25)00522-9 [Epub ahead of print].
The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.
Additional Links: PMID-39954444
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PubMed:
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@article {pmid39954444,
year = {2025},
author = {He, M and Tang, R and Guan, F and Peng, W and Lu, J and Li, K and Zhou, L and Wang, Y and Yuan, Y},
title = {Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137608},
doi = {10.1016/j.jhazmat.2025.137608},
pmid = {39954444},
issn = {1873-3336},
abstract = {The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.},
}
RevDate: 2025-02-15
Microbial Dysbiosis, Titanium Release, and Peri-implantitis.
Journal of dental research [Epub ahead of print].
The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.
Additional Links: PMID-39953673
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@article {pmid39953673,
year = {2025},
author = {Kotsakis, GA and Ganesan, SM},
title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241307939},
doi = {10.1177/00220345241307939},
pmid = {39953673},
issn = {1544-0591},
abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.},
}
RevDate: 2025-02-14
Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.
Trends in plant science pii:S1360-1385(25)00032-9 [Epub ahead of print].
Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.
Additional Links: PMID-39952886
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@article {pmid39952886,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.011},
pmid = {39952886},
issn = {1878-4372},
abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Exploring viral diversity in fermented vegetables through viral metagenomics.
Food microbiology, 128:104733.
Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.
Additional Links: PMID-39952771
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PubMed:
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@article {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Metagenomics
*Vegetables/virology/microbiology
*Fermentation
*Bacteriophages/genetics/isolation & purification/classification
Microbiota
Brassica/microbiology/virology
Fermented Foods/microbiology/virology
Bacteria/genetics/classification/isolation & purification/virology
Biodiversity
Daucus carota/microbiology/virology
Food Microbiology
Viruses/isolation & purification/classification/genetics
Enterobacteriaceae/isolation & purification/genetics/virology/classification
Metagenome
Lactobacillaceae/isolation & purification/genetics/classification
RevDate: 2025-02-14
CmpDate: 2025-02-14
The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.
Food microbiology, 128:104708.
Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.
Additional Links: PMID-39952743
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PubMed:
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@article {pmid39952743,
year = {2025},
author = {Wu, Y and Ma, F and Tan, S and Niu, A and Chen, Y and Liu, Y and Qiu, W and Wang, G},
title = {The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104708},
doi = {10.1016/j.fm.2024.104708},
pmid = {39952743},
issn = {1095-9998},
mesh = {Animals ; *Pseudomonas fragi/genetics/metabolism/growth & development ; *Chickens/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Food Microbiology ; *Meat/microbiology ; Mutation ; Biofilms/growth & development ; Microbiota ; Food Storage ; Food Contamination/analysis ; },
abstract = {Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.},
}
MeSH Terms:
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hide MeSH Terms
Animals
*Pseudomonas fragi/genetics/metabolism/growth & development
*Chickens/microbiology
*Bacterial Proteins/genetics/metabolism
*Food Microbiology
*Meat/microbiology
Mutation
Biofilms/growth & development
Microbiota
Food Storage
Food Contamination/analysis
RevDate: 2025-02-14
CmpDate: 2025-02-14
Turbulent mixing controls fixation of growing antagonistic populations.
Proceedings of the National Academy of Sciences of the United States of America, 122(7):e2417075122.
Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.
Additional Links: PMID-39951503
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PubMed:
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@article {pmid39951503,
year = {2025},
author = {Bauermann, J and Benzi, R and Nelson, DR and Shankar, S and Toschi, F},
title = {Turbulent mixing controls fixation of growing antagonistic populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {7},
pages = {e2417075122},
doi = {10.1073/pnas.2417075122},
pmid = {39951503},
issn = {1091-6490},
mesh = {*Models, Biological ; Population Dynamics ; Computer Simulation ; },
abstract = {Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.},
}
MeSH Terms:
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*Models, Biological
Population Dynamics
Computer Simulation
RevDate: 2025-02-14
CmpDate: 2025-02-14
Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.
Ecological applications : a publication of the Ecological Society of America, 35(1):e70007.
As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.
Additional Links: PMID-39950593
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PubMed:
Citation:
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@article {pmid39950593,
year = {2025},
author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME},
title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {35},
number = {1},
pages = {e70007},
doi = {10.1002/eap.70007},
pmid = {39950593},
issn = {1051-0761},
support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; },
mesh = {*Soil Microbiology ; *Trees ; *Fungi/physiology ; Environmental Restoration and Remediation/methods ; Microbiota ; Conservation of Natural Resources/methods ; },
abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Soil Microbiology
*Trees
*Fungi/physiology
Environmental Restoration and Remediation/methods
Microbiota
Conservation of Natural Resources/methods
RevDate: 2025-02-13
CmpDate: 2025-02-13
Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.
Environmental monitoring and assessment, 197(3):287.
This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.
Additional Links: PMID-39945937
PubMed:
Citation:
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@article {pmid39945937,
year = {2025},
author = {Gharbi, D and Neumann, FH and Staats, J and McDonald, M and Linde, JH and Mmatladi, T and Podile, K and Piketh, S and Burger, R and Garland, RM and Bester, P and Lebre, PH and Ricci, C},
title = {Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {3},
pages = {287},
pmid = {39945937},
issn = {1573-2959},
support = {ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; },
mesh = {Humans ; South Africa/epidemiology ; Male ; Adult ; *Allergens ; Pilot Projects ; Female ; Young Adult ; Adolescent ; Prevalence ; Middle Aged ; *Air Pollutants/analysis ; Pollen ; Hypersensitivity/epidemiology ; Skin Tests ; },
abstract = {This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
South Africa/epidemiology
Male
Adult
*Allergens
Pilot Projects
Female
Young Adult
Adolescent
Prevalence
Middle Aged
*Air Pollutants/analysis
Pollen
Hypersensitivity/epidemiology
Skin Tests
RevDate: 2025-02-13
CmpDate: 2025-02-13
The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.
Microbial ecology, 88(1):4.
Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.
Additional Links: PMID-39945839
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Citation:
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@article {pmid39945839,
year = {2025},
author = {Márquez-Sanz, R and Garrido-Benavent, I and Durán, J and de Los Ríos, A},
title = {The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {4},
pmid = {39945839},
issn = {1432-184X},
support = {PID2019-105469RB-C22//AEI, MICINN/ ; PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigación/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Científicas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; *Soil/chemistry ; Phylogeny ; Chlorophyta ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; },
abstract = {Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Soil Microbiology
Antarctic Regions
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Microbiota
*Soil/chemistry
Phylogeny
Chlorophyta
Nitrogen/analysis/metabolism
Carbon/analysis/metabolism
RevDate: 2025-02-13
Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.
Animals : an open access journal from MDPI, 15(3): pii:ani15030361.
The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.
Additional Links: PMID-39943131
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PubMed:
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@article {pmid39943131,
year = {2025},
author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL},
title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/ani15030361},
pmid = {39943131},
issn = {2076-2615},
abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.},
}
RevDate: 2025-02-13
Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.
Materials (Basel, Switzerland), 18(3): pii:ma18030625.
This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.
Additional Links: PMID-39942291
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@article {pmid39942291,
year = {2025},
author = {Santás-Miguel, V and Lalín-Pousa, V and Conde-Cid, M and Rodríguez-Seijo, A and Pérez-Rodríguez, P},
title = {Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.},
journal = {Materials (Basel, Switzerland)},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/ma18030625},
pmid = {39942291},
issn = {1996-1944},
support = {ED481D-2021/016//Consellería de Cultura, Educación e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovación y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovación y Universidades/ ; 101112754//MRV4SOC project/ ; ED481B-2022-081//Xunta de Galicia/ ; },
abstract = {This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.},
}
RevDate: 2025-02-13
Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.
Foods (Basel, Switzerland), 14(3): pii:foods14030469.
Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.
Additional Links: PMID-39942061
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PubMed:
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@article {pmid39942061,
year = {2025},
author = {Di Biase, M and Scicchitano, D and Valerio, F and Lonigro, SL and Cifarelli, V and Ostante, G and D'Antuono, I and Candela, M and Ferrara, M},
title = {Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030469},
pmid = {39942061},
issn = {2304-8158},
support = {MicroBHE Project//IBISBA - IT/ ; DAB.AD005.225//FOE - 2021/ ; },
abstract = {Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.},
}
RevDate: 2025-02-12
CmpDate: 2025-02-12
Distribution of Bacillota in Water and Sediments from Aquatic Environments.
Microbial ecology, 88(1):3.
The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.
Additional Links: PMID-39937305
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Citation:
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@article {pmid39937305,
year = {2025},
author = {Argentino, ICV and Godoy, MG and Seldin, L and Jurelevicius, D},
title = {Distribution of Bacillota in Water and Sediments from Aquatic Environments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {3},
pmid = {39937305},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; Microbiota ; Phylogeny ; Fresh Water/microbiology ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; },
abstract = {The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.},
}
MeSH Terms:
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hide MeSH Terms
*Geologic Sediments/microbiology
Brazil
*RNA, Ribosomal, 16S/genetics
Seawater/microbiology
Water Microbiology
Microbiota
Phylogeny
Fresh Water/microbiology
Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics
RevDate: 2025-02-12
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.
Molecular ecology resources [Epub ahead of print].
Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.
Additional Links: PMID-39936183
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@article {pmid39936183,
year = {2025},
author = {Brait, N and Hackl, T and Lequime, S},
title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14083},
doi = {10.1111/1755-0998.14083},
pmid = {39936183},
issn = {1755-0998},
abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.},
}
RevDate: 2025-02-12
CmpDate: 2025-02-12
Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.
Journal of environmental management, 375:124223.
Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.
Additional Links: PMID-39935057
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@article {pmid39935057,
year = {2025},
author = {Ruiz-Ruiz, P and Mohedano-Caballero, P and De Vrieze, J},
title = {Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124223},
doi = {10.1016/j.jenvman.2025.124223},
pmid = {39935057},
issn = {1095-8630},
mesh = {*Biofuels ; *Microalgae/metabolism/growth & development ; *Amino Acids, Diamino/metabolism ; *Methane/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.},
}
MeSH Terms:
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*Biofuels
*Microalgae/metabolism/growth & development
*Amino Acids, Diamino/metabolism
*Methane/metabolism
Carbon Dioxide/metabolism
RevDate: 2025-02-11
Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] [Epub ahead of print].
Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.
Additional Links: PMID-39934529
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@article {pmid39934529,
year = {2025},
author = {Roy, R and Das, A and Ganguly, D and Chakraborty, P and Paul, P and Das, S and Maity, A and Malik, M and Tribedi, P},
title = {Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39934529},
issn = {1678-4405},
support = {TNU/R&D/M/11//The Neotia University/ ; },
abstract = {Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.},
}
RevDate: 2025-02-11
CmpDate: 2025-02-11
Habitat fragmentation enhances microbial collective defence.
Journal of the Royal Society, Interface, 22(223):20240611.
Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.
Additional Links: PMID-39933594
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@article {pmid39933594,
year = {2025},
author = {Verdon, N and Popescu, O and Titmuss, S and Allen, RJ},
title = {Habitat fragmentation enhances microbial collective defence.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {223},
pages = {20240611},
doi = {10.1098/rsif.2024.0611},
pmid = {39933594},
issn = {1742-5662},
support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; },
mesh = {*Ecosystem ; *Models, Biological ; Bacteria/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.},
}
MeSH Terms:
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*Ecosystem
*Models, Biological
Bacteria/metabolism
Anti-Bacterial Agents/pharmacology
RevDate: 2025-02-10
CmpDate: 2025-02-10
Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.
International journal of systematic and evolutionary microbiology, 75(2):.
In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.
Additional Links: PMID-39928396
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@article {pmid39928396,
year = {2025},
author = {Nakajima, M and Nakai, R and Hirakata, Y and Kubota, K and Satoh, H and Nobu, MK and Narihiro, T and Kuroda, K},
title = {Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.006668},
pmid = {39928396},
issn = {1466-5034},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; *Sequence Analysis, DNA ; *Base Composition ; Bacterial Typing Techniques ; Fatty Acids ; Symbiosis ; DNA, Archaeal/genetics ; },
abstract = {In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.},
}
MeSH Terms:
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*Phylogeny
*RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics
*Sequence Analysis, DNA
*Base Composition
Bacterial Typing Techniques
Fatty Acids
Symbiosis
DNA, Archaeal/genetics
RevDate: 2025-02-09
CmpDate: 2025-02-09
Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.
BMC biology, 23(1):40.
BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.
RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.
CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.
Additional Links: PMID-39924526
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@article {pmid39924526,
year = {2025},
author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C},
title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {40},
pmid = {39924526},
issn = {1741-7007},
support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Microbiota ; Humans ; *Odorants/analysis ; Laundering/methods ; Volatile Organic Compounds/analysis ; Clothing ; Skin/microbiology ; },
abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.
RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.
CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.},
}
MeSH Terms:
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*Microbiota
Humans
*Odorants/analysis
Laundering/methods
Volatile Organic Compounds/analysis
Clothing
Skin/microbiology
RevDate: 2025-02-06
CmpDate: 2025-02-06
Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.
Scientific reports, 15(1):4459.
Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.
Additional Links: PMID-39915510
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Citation:
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@article {pmid39915510,
year = {2025},
author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ},
title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4459},
pmid = {39915510},
issn = {2045-2322},
mesh = {*Anthozoa/microbiology ; Animals ; Malaysia ; *Microbiota ; *Symbiosis ; Biodiversity ; Bacteria/genetics/classification ; Climate Change ; Coral Reefs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.},
}
MeSH Terms:
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hide MeSH Terms
*Anthozoa/microbiology
Animals
Malaysia
*Microbiota
*Symbiosis
Biodiversity
Bacteria/genetics/classification
Climate Change
Coral Reefs
Phylogeny
RNA, Ribosomal, 16S/genetics
RevDate: 2025-02-06
MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.
FEMS microbiology letters pii:8003766 [Epub ahead of print].
Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early-career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this three-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement like hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.
Additional Links: PMID-39914458
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@article {pmid39914458,
year = {2025},
author = {Wenger, A and Bakkeren, E and Granato, E and Tecon, R and Mitri, S and Möbius, W},
title = {MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf022},
pmid = {39914458},
issn = {1574-6968},
abstract = {Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early-career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this three-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement like hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.},
}
RevDate: 2025-02-06
Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.
Journal of environmental management, 376:124382 pii:S0301-4797(25)00358-5 [Epub ahead of print].
Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.
Additional Links: PMID-39914213
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@article {pmid39914213,
year = {2025},
author = {Ma, R and Huang, Z and Jiang, Y and Zhao, A and Yu, G and Lin, C and Zhu, L and Zhang, X and Li, X and Wang, C},
title = {Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124382},
doi = {10.1016/j.jenvman.2025.124382},
pmid = {39914213},
issn = {1095-8630},
abstract = {Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.},
}
RevDate: 2025-02-06
CmpDate: 2025-02-06
Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.
Science (New York, N.Y.), 387(6734):609-615.
Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.
Additional Links: PMID-39913585
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@article {pmid39913585,
year = {2025},
author = {Pertierra, LR and Convey, P and Barbosa, A and Biersma, EM and Cowan, D and Diniz-Filho, JAF and de Los Ríos, A and Escribano-Álvarez, P and Fraser, CI and Fontaneto, D and Greve, M and Griffiths, HJ and Harris, M and Hughes, KA and Lynch, HJ and Ladle, RJ and Liu, XP and le Roux, PC and Majewska, R and Molina-Montenegro, MA and Peck, LS and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, LG and Terauds, A and Varliero, G and Vianna, JA and Wilmotte, A and Chown, SL and Olalla-Tárraga, MÁ and Hortal, J},
title = {Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6734},
pages = {609-615},
doi = {10.1126/science.adk2118},
pmid = {39913585},
issn = {1095-9203},
mesh = {Antarctic Regions ; *Biodiversity ; Animals ; *Fresh Water ; *Invertebrates/physiology ; Vertebrates/physiology ; Biological Evolution ; Plants ; Conservation of Natural Resources ; },
abstract = {Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.},
}
MeSH Terms:
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hide MeSH Terms
Antarctic Regions
*Biodiversity
Animals
*Fresh Water
*Invertebrates/physiology
Vertebrates/physiology
Biological Evolution
Plants
Conservation of Natural Resources
RevDate: 2025-02-06
Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.
Applied and environmental microbiology [Epub ahead of print].
Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.
Additional Links: PMID-39912641
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@article {pmid39912641,
year = {2025},
author = {Hamovit, N and RoyChowdhury, T and Akob, DM and Zhang, X and McCarty, G and Yarwood, S},
title = {Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0216124},
doi = {10.1128/aem.02161-24},
pmid = {39912641},
issn = {1098-5336},
abstract = {Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.},
}
RevDate: 2025-02-06
Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.
Journal of microbiology & biology education [Epub ahead of print].
In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.
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@article {pmid39912591,
year = {2025},
author = {Porras-Socias, P and Mattiussi, R and Silveira, KA and O'Flaherty, V},
title = {Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0011624},
doi = {10.1128/jmbe.00116-24},
pmid = {39912591},
issn = {1935-7877},
abstract = {In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.},
}
RevDate: 2025-02-06
Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.
Water research X, 27:100304.
Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.
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@article {pmid39911734,
year = {2025},
author = {Jia, C and Li, J and Li, Z and Zhang, L},
title = {Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.},
journal = {Water research X},
volume = {27},
number = {},
pages = {100304},
pmid = {39911734},
issn = {2589-9147},
abstract = {Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.},
}
RevDate: 2025-02-06
Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.
Current research in food science, 10:100976.
Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.
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@article {pmid39911603,
year = {2025},
author = {Sikombe, TW and Linnemann, AR and Moonga, HB and Quilitz, S and Schoustra, SE and Smid, EJ and Alekseeva, A},
title = {Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.},
journal = {Current research in food science},
volume = {10},
number = {},
pages = {100976},
pmid = {39911603},
issn = {2665-9271},
abstract = {Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.},
}
RevDate: 2025-02-06
Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.
Frontiers in veterinary science, 11:1522917.
The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.
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@article {pmid39911488,
year = {2024},
author = {Vaselek, S and Alten, B},
title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1522917},
pmid = {39911488},
issn = {2297-1769},
abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.},
}
RevDate: 2025-02-05
CmpDate: 2025-02-05
Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.
Microbial ecology, 88(1):2.
Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.
Additional Links: PMID-39909903
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@article {pmid39909903,
year = {2025},
author = {Panico, SC and Alberti, G and Foscari, A and Sciabbarrasi, GL and Tomao, A and Incerti, G},
title = {Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {2},
pmid = {39909903},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/genetics/classification ; *Bacteria/classification/genetics/isolation & purification ; *Grassland ; Italy ; *Biodiversity ; *Carbon/analysis ; Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Climate Change ; Mycobiome ; },
abstract = {Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.},
}
MeSH Terms:
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hide MeSH Terms
*Soil Microbiology
*Soil/chemistry
*Fungi/genetics/classification
*Bacteria/classification/genetics/isolation & purification
*Grassland
Italy
*Biodiversity
*Carbon/analysis
Microbiota
Nitrogen/analysis
Phosphorus/analysis
Forests
Hydrogen-Ion Concentration
Climate Change
Mycobiome
RevDate: 2025-02-05
Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.
Folia microbiologica [Epub ahead of print].
In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.
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@article {pmid39907926,
year = {2025},
author = {Breedt, G and Korsten, L and Gokul, JK},
title = {Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39907926},
issn = {1874-9356},
abstract = {In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.},
}
RevDate: 2025-02-05
CmpDate: 2025-02-05
Enhancing microbial predator-prey detection with network and trait-based analyses.
Microbiome, 13(1):37.
BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.
RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.
CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.
Additional Links: PMID-39905550
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@article {pmid39905550,
year = {2025},
author = {Martínez Rendón, C and Braun, C and Kappelsberger, M and Boy, J and Casanova-Katny, A and Glaser, K and Dumack, K},
title = {Enhancing microbial predator-prey detection with network and trait-based analyses.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {37},
pmid = {39905550},
issn = {2049-2618},
mesh = {Animals ; *Microbiota ; Antarctic Regions ; Food Chain ; Predatory Behavior ; },
abstract = {BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.
RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.
CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.},
}
MeSH Terms:
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Animals
*Microbiota
Antarctic Regions
Food Chain
Predatory Behavior
RevDate: 2025-02-04
Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).
Microbiological research, 293:128084 pii:S0944-5013(25)00040-0 [Epub ahead of print].
Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.
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@article {pmid39903999,
year = {2025},
author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A},
title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128084},
doi = {10.1016/j.micres.2025.128084},
pmid = {39903999},
issn = {1618-0623},
abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.},
}
RevDate: 2025-02-04
In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.
Microbiology spectrum [Epub ahead of print].
UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.
IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.
Additional Links: PMID-39902955
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PubMed:
Citation:
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@article {pmid39902955,
year = {2025},
author = {Li, Q and Marietou, A and Andersen, FF and Hosek, J and Scavenius, C and Zhang, J and Schwab, C},
title = {In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219324},
doi = {10.1128/spectrum.02193-24},
pmid = {39902955},
issn = {2165-0497},
abstract = {UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.
IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.},
}
RevDate: 2025-02-03
CmpDate: 2025-02-03
Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.
PeerJ, 13:e18807.
Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.
Additional Links: PMID-39897492
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Citation:
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@article {pmid39897492,
year = {2025},
author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C},
title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18807},
pmid = {39897492},
issn = {2167-8359},
mesh = {*Porifera/microbiology ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Porifera/microbiology
*Microbiota
Animals
*Fresh Water/microbiology
North Carolina
*Symbiosis
Bacteria/classification/genetics/isolation & purification
RevDate: 2025-01-31
CmpDate: 2025-01-31
Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.
Microbial ecology, 88(1):1.
Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.
Additional Links: PMID-39890664
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Citation:
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@article {pmid39890664,
year = {2025},
author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L},
title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {1},
pmid = {39890664},
issn = {1432-184X},
support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; },
mesh = {*Capsicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endophytes/isolation & purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; },
abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Capsicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Endophytes/isolation & purification/classification/physiology/genetics
Plant Diseases/microbiology
Plant Roots/microbiology
Fungi/classification/genetics/isolation & purification/physiology
RevDate: 2025-01-31
CmpDate: 2025-01-31
The Microbiome and Pulmonary Immune Function.
Clinics in chest medicine, 46(1):77-91.
In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.
Additional Links: PMID-39890294
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PubMed:
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@article {pmid39890294,
year = {2025},
author = {Baker, JM and Dickson, RP},
title = {The Microbiome and Pulmonary Immune Function.},
journal = {Clinics in chest medicine},
volume = {46},
number = {1},
pages = {77-91},
doi = {10.1016/j.ccm.2024.10.006},
pmid = {39890294},
issn = {1557-8216},
mesh = {Humans ; *Microbiota/immunology/physiology ; *Lung/microbiology/immunology ; Lung Diseases/immunology/microbiology ; },
abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.},
}
MeSH Terms:
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Humans
*Microbiota/immunology/physiology
*Lung/microbiology/immunology
Lung Diseases/immunology/microbiology
RevDate: 2025-01-31
Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.
Journal of hazardous materials, 488:137399 pii:S0304-3894(25)00311-5 [Epub ahead of print].
Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.
Additional Links: PMID-39889603
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PubMed:
Citation:
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@article {pmid39889603,
year = {2025},
author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P},
title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137399},
doi = {10.1016/j.jhazmat.2025.137399},
pmid = {39889603},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.},
}
RevDate: 2025-02-01
CmpDate: 2025-02-01
The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.
Journal of evolutionary biology, 38(2):180-189.
Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.
Additional Links: PMID-39587684
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PubMed:
Citation:
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@article {pmid39587684,
year = {2025},
author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS},
title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {2},
pages = {180-189},
doi = {10.1093/jeb/voae143},
pmid = {39587684},
issn = {1420-9101},
support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; },
mesh = {Animals ; *Drosophila/microbiology/genetics ; *Phylogeny ; *Diet ; *Desert Climate ; *Microbiota ; Bacteria/genetics/classification ; Symbiosis ; Arizona ; },
abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Drosophila/microbiology/genetics
*Phylogeny
*Diet
*Desert Climate
*Microbiota
Bacteria/genetics/classification
Symbiosis
Arizona
RevDate: 2025-01-30
Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.
Scientific reports, 15(1):3796 pii:10.1038/s41598-025-87051-2.
Additional Links: PMID-39885242
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PubMed:
Citation:
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@article {pmid39885242,
year = {2025},
author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N},
title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3796},
doi = {10.1038/s41598-025-87051-2},
pmid = {39885242},
issn = {2045-2322},
}
RevDate: 2025-01-30
Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.
Microbiological research, 293:128076 pii:S0944-5013(25)00032-1 [Epub ahead of print].
Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.
Additional Links: PMID-39884152
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PubMed:
Citation:
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@article {pmid39884152,
year = {2025},
author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128076},
doi = {10.1016/j.micres.2025.128076},
pmid = {39884152},
issn = {1618-0623},
abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.},
}
RevDate: 2025-01-30
Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.
Advanced biotechnology, 2(3):26.
Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.
Additional Links: PMID-39883228
PubMed:
Citation:
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@article {pmid39883228,
year = {2024},
author = {Han, JR and Li, S and Li, WJ and Dong, L},
title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.},
journal = {Advanced biotechnology},
volume = {2},
number = {3},
pages = {26},
pmid = {39883228},
issn = {2948-2801},
support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; },
abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.},
}
RevDate: 2025-01-30
Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.
Applied and environmental microbiology [Epub ahead of print].
UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.
IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.
Additional Links: PMID-39882875
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PubMed:
Citation:
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@article {pmid39882875,
year = {2025},
author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL},
title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0236824},
doi = {10.1128/aem.02368-24},
pmid = {39882875},
issn = {1098-5336},
abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.
IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.},
}
RevDate: 2025-01-30
Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.
Microbiology spectrum [Epub ahead of print].
The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.
Additional Links: PMID-39882867
Publisher:
PubMed:
Citation:
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@article {pmid39882867,
year = {2025},
author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR},
title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0220924},
doi = {10.1128/spectrum.02209-24},
pmid = {39882867},
issn = {2165-0497},
abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.},
}
RevDate: 2025-01-29
CmpDate: 2025-01-29
Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.
Microbial ecology, 87(1):181.
Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.
Additional Links: PMID-39880965
PubMed:
Citation:
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@article {pmid39880965,
year = {2025},
author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A},
title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {181},
pmid = {39880965},
issn = {1432-184X},
support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Agave/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; *Agriculture ; *RNA, Ribosomal, 16S/genetics ; Mexico ; Alcoholic Beverages/microbiology ; Biodiversity ; Rhizosphere ; },
abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Agave/microbiology
*Soil Microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
*Agriculture
*RNA, Ribosomal, 16S/genetics
Mexico
Alcoholic Beverages/microbiology
Biodiversity
Rhizosphere
RevDate: 2025-01-29
PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.
Molecular & cellular proteomics : MCP pii:S1535-9476(25)00016-7 [Epub ahead of print].
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a case study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.
Additional Links: PMID-39880083
Publisher:
PubMed:
Citation:
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@article {pmid39880083,
year = {2025},
author = {Moortele, TV and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100918},
doi = {10.1016/j.mcpro.2025.100918},
pmid = {39880083},
issn = {1535-9484},
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a case study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}
RevDate: 2025-01-29
Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.
mBio [Epub ahead of print].
UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.
IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.
Additional Links: PMID-39878512
Publisher:
PubMed:
Citation:
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@article {pmid39878512,
year = {2025},
author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC},
title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.},
journal = {mBio},
volume = {},
number = {},
pages = {e0392824},
doi = {10.1128/mbio.03928-24},
pmid = {39878512},
issn = {2150-7511},
abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.
IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.},
}
RevDate: 2025-01-29
Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.
Journal of microbiology & biology education [Epub ahead of print].
We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.
Additional Links: PMID-39878482
Publisher:
PubMed:
Citation:
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@article {pmid39878482,
year = {2025},
author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J},
title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0005624},
doi = {10.1128/jmbe.00056-24},
pmid = {39878482},
issn = {1935-7877},
abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.},
}
RevDate: 2025-01-29
CmpDate: 2025-01-29
Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.
Clinical implant dentistry and related research, 27(1):e13423.
BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.
METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.
RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p < 0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.
CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.
Additional Links: PMID-39876091
Publisher:
PubMed:
Citation:
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@article {pmid39876091,
year = {2025},
author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI},
title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.},
journal = {Clinical implant dentistry and related research},
volume = {27},
number = {1},
pages = {e13423},
doi = {10.1111/cid.13423},
pmid = {39876091},
issn = {1708-8208},
support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; },
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Female ; Male ; *Dental Implants/microbiology/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; },
abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.
METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.
RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p < 0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.
CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Peri-Implantitis/microbiology
*Microbiota
Cross-Sectional Studies
Female
Male
*Dental Implants/microbiology/adverse effects
Middle Aged
RNA, Ribosomal, 16S/analysis
Adult
Aged
RevDate: 2025-01-28
Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.
Plant disease [Epub ahead of print].
Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.
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@article {pmid39874167,
year = {2025},
author = {Zhang, F and Zhang, S and Wu, Y and Liu, J and Zhao, S and Qiu, Z and Zhu 朱, M墨},
title = {Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-12-24-2632-PDN},
pmid = {39874167},
issn = {0191-2917},
abstract = {Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.},
}
RevDate: 2025-01-28
Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.
Microbial ecology, 87(1):180 pii:10.1007/s00248-025-02498-0.
Additional Links: PMID-39873755
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@article {pmid39873755,
year = {2025},
author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE},
title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {180},
doi = {10.1007/s00248-025-02498-0},
pmid = {39873755},
issn = {1432-184X},
}
RevDate: 2025-01-28
CmpDate: 2025-01-28
Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.
Environmental microbiology reports, 17(1):e70069.
Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.
Additional Links: PMID-39871445
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@article {pmid39871445,
year = {2025},
author = {Zahir, Z and Khan, F and Hall, BD},
title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70069},
doi = {10.1111/1758-2229.70069},
pmid = {39871445},
issn = {1758-2229},
support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; },
mesh = {*Wetlands ; *Carbon/metabolism/analysis ; *Sulfates/metabolism ; *Ponds/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Phylogeny ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Wetlands
*Carbon/metabolism/analysis
*Sulfates/metabolism
*Ponds/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Phylogeny
Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Biodiversity
RevDate: 2025-01-28
CmpDate: 2025-01-28
Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.
Environmental microbiology, 27(1):e70032.
Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.
Additional Links: PMID-39871406
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@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}
MeSH Terms:
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hide MeSH Terms
Antarctic Regions
*Soil Microbiology
*Archaea/classification/genetics
*Bacteria/classification/isolation & purification/genetics
*Ecosystem
Microbiota
Phylogeny
Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics
RevDate: 2025-01-27
CmpDate: 2025-01-27
Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.
Microbial ecology, 87(1):177.
The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.
Additional Links: PMID-39871020
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@article {pmid39871020,
year = {2025},
author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J},
title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {177},
pmid = {39871020},
issn = {1432-184X},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Forests ; *Carbon/metabolism ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Organic Chemicals/metabolism ; Microbial Interactions ; },
abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.},
}
MeSH Terms:
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*Soil Microbiology
*Soil/chemistry
*Forests
*Carbon/metabolism
Hydrogen-Ion Concentration
China
*Microbiota
Carbon Cycle
Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Organic Chemicals/metabolism
Microbial Interactions
RevDate: 2025-01-27
CmpDate: 2025-01-27
A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.
Microbial ecology, 87(1):179.
The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.
Additional Links: PMID-39870904
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@article {pmid39870904,
year = {2025},
author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P},
title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {179},
pmid = {39870904},
issn = {1432-184X},
mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Reunion ; *Fungi/classification/genetics/isolation & purification/metabolism ; Seawater/microbiology ; Indian Ocean ; Seasons ; Biodiversity ; Environmental Monitoring/methods ; Islands ; Microalgae/classification/metabolism ; Geologic Sediments/microbiology ; },
abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.},
}
MeSH Terms:
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*Coral Reefs
*Microbiota
*Anthozoa/microbiology
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
Reunion
*Fungi/classification/genetics/isolation & purification/metabolism
Seawater/microbiology
Indian Ocean
Seasons
Biodiversity
Environmental Monitoring/methods
Islands
Microalgae/classification/metabolism
Geologic Sediments/microbiology
RevDate: 2025-01-27
CmpDate: 2025-01-27
The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.
Microbial ecology, 87(1):178.
In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.
Additional Links: PMID-39870843
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@article {pmid39870843,
year = {2025},
author = {Li, Q and Shao, H},
title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {178},
pmid = {39870843},
issn = {1432-184X},
support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; *Soil Microbiology ; Host-Pathogen Interactions ; Bacteria/genetics/metabolism ; },
abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.},
}
MeSH Terms:
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*Introduced Species
*Plants/microbiology
*Plant Diseases/microbiology
*Soil Microbiology
Host-Pathogen Interactions
Bacteria/genetics/metabolism
RevDate: 2025-01-27
Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.
bioRxiv : the preprint server for biology pii:2025.01.15.633187.
The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.
Additional Links: PMID-39868213
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@article {pmid39868213,
year = {2025},
author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM},
title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.15.633187},
pmid = {39868213},
issn = {2692-8205},
abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.},
}
RevDate: 2025-01-27
Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.
bioRxiv : the preprint server for biology pii:2025.01.14.632972.
Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans , and Streptococcus sanguinis . Gene fragments, developed to contain the constitutive promoter P veg , the fluorescent gene of interest as well as aad9 , providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis , were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans , and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.
Additional Links: PMID-39868180
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@article {pmid39868180,
year = {2025},
author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR},
title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.14.632972},
pmid = {39868180},
issn = {2692-8205},
abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans , and Streptococcus sanguinis . Gene fragments, developed to contain the constitutive promoter P veg , the fluorescent gene of interest as well as aad9 , providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis , were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans , and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.},
}
RevDate: 2025-01-25
doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.
Bioinformatics (Oxford, England) pii:7979242 [Epub ahead of print].
SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.
doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.
Additional Links: PMID-39862387
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@article {pmid39862387,
year = {2025},
author = {Almeida-Silva, F and Van de Peer, Y},
title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf043},
pmid = {39862387},
issn = {1367-4811},
abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.
doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.},
}
RevDate: 2025-01-25
Genetic and species rearrangements in microbial consortia impact biodegradation potential.
The ISME journal pii:7979093 [Epub ahead of print].
Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.
Additional Links: PMID-39861970
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@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}
RevDate: 2025-01-25
Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.
Biology, 14(1): pii:biology14010028.
The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.
Additional Links: PMID-39857259
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@article {pmid39857259,
year = {2025},
author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH},
title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biology14010028},
pmid = {39857259},
issn = {2079-7737},
support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; },
abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.},
}
RevDate: 2025-01-24
CmpDate: 2025-01-24
Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.
Scientific reports, 15(1):3152.
Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.
Additional Links: PMID-39856188
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@article {pmid39856188,
year = {2025},
author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D},
title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3152},
pmid = {39856188},
issn = {2045-2322},
support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; },
mesh = {*Microcystis/virology/physiology ; *Bacteriophages/physiology ; *Fresh Water/virology ; Eutrophication ; Ecosystem ; Cyanobacteria/virology/physiology ; Photosynthesis ; Host Specificity ; },
abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.},
}
MeSH Terms:
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*Microcystis/virology/physiology
*Bacteriophages/physiology
*Fresh Water/virology
Eutrophication
Ecosystem
Cyanobacteria/virology/physiology
Photosynthesis
Host Specificity
RevDate: 2025-01-24
Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.
Water research, 275:123138 pii:S0043-1354(25)00052-1 [Epub ahead of print].
Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.
Additional Links: PMID-39855017
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@article {pmid39855017,
year = {2025},
author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J},
title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.},
journal = {Water research},
volume = {275},
number = {},
pages = {123138},
doi = {10.1016/j.watres.2025.123138},
pmid = {39855017},
issn = {1879-2448},
abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.},
}
RevDate: 2025-01-24
Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.
Journal of environmental management, 375:124203 pii:S0301-4797(25)00179-3 [Epub ahead of print].
Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.
Additional Links: PMID-39854900
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@article {pmid39854900,
year = {2025},
author = {Reid, CJ and Farrell, M and Kirby, JK},
title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124203},
doi = {10.1016/j.jenvman.2025.124203},
pmid = {39854900},
issn = {1095-8630},
abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.},
}
RevDate: 2025-01-24
CmpDate: 2025-01-24
More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.
Microbial ecology, 87(1):176.
With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.
Additional Links: PMID-39853499
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@article {pmid39853499,
year = {2025},
author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC},
title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {176},
pmid = {39853499},
issn = {1432-184X},
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Italy ; Fungi/classification/isolation & purification/genetics ; Hydrogen-Ion Concentration ; Batrachochytrium ; Wetlands ; Temperature ; },
abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Skin/microbiology
*Microbiota
*Ecosystem
*Anura/microbiology
*Bacteria/classification/genetics/isolation & purification
Italy
Fungi/classification/isolation & purification/genetics
Hydrogen-Ion Concentration
Batrachochytrium
Wetlands
Temperature
RevDate: 2025-01-24
Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.
The ISME journal pii:7978262 [Epub ahead of print].
One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.
Additional Links: PMID-39849986
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@article {pmid39849986,
year = {2025},
author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z},
title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf012},
pmid = {39849986},
issn = {1751-7370},
abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.},
}
RevDate: 2025-01-23
CmpDate: 2025-01-23
The influence of depth on the global deep-sea plasmidome.
Scientific reports, 15(1):2959.
Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.
Additional Links: PMID-39849009
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@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; Metagenome ; Seawater/microbiology ; Ecosystem ; Oceans and Seas ; Gammaproteobacteria/genetics/classification ; Alphaproteobacteria/genetics ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}
MeSH Terms:
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*Plasmids/genetics
Metagenome
Seawater/microbiology
Ecosystem
Oceans and Seas
Gammaproteobacteria/genetics/classification
Alphaproteobacteria/genetics
RevDate: 2025-01-23
Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.
Journal of environmental management, 375:124191 pii:S0301-4797(25)00167-7 [Epub ahead of print].
Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.
Additional Links: PMID-39848193
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@article {pmid39848193,
year = {2025},
author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F},
title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124191},
doi = {10.1016/j.jenvman.2025.124191},
pmid = {39848193},
issn = {1095-8630},
abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.},
}
RevDate: 2025-01-23
CmpDate: 2025-01-23
Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.
Proceedings of the National Academy of Sciences of the United States of America, 122(4):e2414434122.
Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.
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@article {pmid39847340,
year = {2025},
author = {Ganley, JG and Seyedsayamdost, MR},
title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {4},
pages = {e2414434122},
doi = {10.1073/pnas.2414434122},
pmid = {39847340},
issn = {1091-6490},
support = {Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; R35 GM152049/GM/NIGMS NIH HHS/United States ; },
mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Cell Membrane/metabolism ; Seaweed/metabolism ; Symbiosis/physiology ; },
abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.},
}
MeSH Terms:
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*Roseobacter/metabolism
*Iron/metabolism
Cell Membrane/metabolism
Seaweed/metabolism
Symbiosis/physiology
RevDate: 2025-01-23
Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.
Frontiers in plant science, 15:1476142.
Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.
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@article {pmid39845484,
year = {2024},
author = {Tóth, VR},
title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1476142},
pmid = {39845484},
issn = {1664-462X},
abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.},
}
RevDate: 2025-01-23
Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.
FEMS microbiology ecology pii:7973005 [Epub ahead of print].
Despite the beneficial effects of Plant Growth-Promoting Rhizobacteria (PGPR) on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 Days After Sowing (DAS). However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.
Additional Links: PMID-39844349
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@article {pmid39844349,
year = {2025},
author = {de Souza, LF and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Romão Dumaresq, AS and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC},
title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf013},
pmid = {39844349},
issn = {1574-6941},
abstract = {Despite the beneficial effects of Plant Growth-Promoting Rhizobacteria (PGPR) on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 Days After Sowing (DAS). However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.},
}
RevDate: 2025-01-23
Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.
FEMS microbiology ecology pii:7973008 [Epub ahead of print].
Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.
Additional Links: PMID-39844346
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@article {pmid39844346,
year = {2025},
author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A},
title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf012},
pmid = {39844346},
issn = {1574-6941},
abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.},
}
RevDate: 2025-01-22
A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.
Scientific data, 12(1):133.
Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.
Additional Links: PMID-39843903
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@article {pmid39843903,
year = {2025},
author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA},
title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {133},
pmid = {39843903},
issn = {2052-4463},
support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.},
}
RevDate: 2025-01-22
The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.
Frontiers in veterinary science, 11:1420282.
INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.
METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.
RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.
DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.
Additional Links: PMID-39840338
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@article {pmid39840338,
year = {2024},
author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C},
title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1420282},
pmid = {39840338},
issn = {2297-1769},
abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.
METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.
RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.
DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.},
}
RevDate: 2025-01-22
CmpDate: 2025-01-22
GOPhage: protein function annotation for bacteriophages by integrating the genomic context.
Briefings in bioinformatics, 26(1):.
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.
Additional Links: PMID-39838963
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@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
MeSH Terms:
show MeSH Terms
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*Bacteriophages/genetics
*Genome, Viral
*Molecular Sequence Annotation
*Viral Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods
Software
RevDate: 2025-01-21
CmpDate: 2025-01-22
The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.
Scientific reports, 15(1):2638.
Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.
Additional Links: PMID-39838210
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Citation:
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@article {pmid39838210,
year = {2025},
author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B},
title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2638},
pmid = {39838210},
issn = {2045-2322},
support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; },
mesh = {Humans ; *Crohn Disease/genetics/pathology ; *Mutation ; Female ; Male ; Serpins/genetics/metabolism ; Apoptosis/genetics ; Exome Sequencing ; Epithelial Cells/metabolism/pathology ; Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation ; Adult ; Cell Movement/genetics ; Twins/genetics ; },
abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.},
}
MeSH Terms:
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Humans
*Crohn Disease/genetics/pathology
*Mutation
Female
Male
Serpins/genetics/metabolism
Apoptosis/genetics
Exome Sequencing
Epithelial Cells/metabolism/pathology
Intestinal Mucosa/metabolism/pathology
Genetic Predisposition to Disease
Cell Proliferation
Adult
Cell Movement/genetics
Twins/genetics
RevDate: 2025-01-21
CmpDate: 2025-01-21
Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.
Microbial ecology, 87(1):175.
Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.
Additional Links: PMID-39838107
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@article {pmid39838107,
year = {2025},
author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM},
title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {175},
pmid = {39838107},
issn = {1432-184X},
support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; },
mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; },
abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.},
}
MeSH Terms:
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*Cheese/microbiology
*Bacteriocins/metabolism/biosynthesis
*Enterococcus/metabolism/genetics
*Microbiota
Biodiversity
Food Microbiology
RNA, Ribosomal, 16S/genetics
Milk/microbiology
Animals
RevDate: 2025-01-22
CmpDate: 2025-01-21
Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.
The ISME journal, 19(1):.
As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.
Additional Links: PMID-39716385
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@article {pmid39716385,
year = {2025},
author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ},
title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39716385},
issn = {1751-7370},
mesh = {*Phytoplankton/genetics/metabolism/growth & development ; *Carbon Dioxide/metabolism ; *Alteromonas/genetics/metabolism ; *Prochlorococcus/genetics/metabolism/growth & development ; Seawater/microbiology ; Coculture Techniques ; Biological Coevolution ; Diatoms/genetics/growth & development/metabolism ; Microbial Interactions ; },
abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.},
}
MeSH Terms:
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*Phytoplankton/genetics/metabolism/growth & development
*Carbon Dioxide/metabolism
*Alteromonas/genetics/metabolism
*Prochlorococcus/genetics/metabolism/growth & development
Seawater/microbiology
Coculture Techniques
Biological Coevolution
Diatoms/genetics/growth & development/metabolism
Microbial Interactions
RevDate: 2025-01-21
CmpDate: 2025-01-21
Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.
Microbial ecology, 87(1):174.
Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.
Additional Links: PMID-39836327
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Citation:
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@article {pmid39836327,
year = {2025},
author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C},
title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {174},
pmid = {39836327},
issn = {1432-184X},
mesh = {*Asparagus Plant/microbiology/growth & development ; *Zea mays/microbiology/growth & development ; *Soil Microbiology ; *Rhizosphere ; *Plant Roots/microbiology/growth & development ; *Bacteria/genetics/classification/isolation & purification/metabolism/growth & development ; *RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Peru ; Phosphates/metabolism ; Salt Tolerance ; Soil/chemistry ; },
abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.},
}
MeSH Terms:
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*Asparagus Plant/microbiology/growth & development
*Zea mays/microbiology/growth & development
*Soil Microbiology
*Rhizosphere
*Plant Roots/microbiology/growth & development
*Bacteria/genetics/classification/isolation & purification/metabolism/growth & development
*RNA, Ribosomal, 16S/genetics
Indoleacetic Acids/metabolism
Peru
Phosphates/metabolism
Salt Tolerance
Soil/chemistry
RevDate: 2025-01-20
CmpDate: 2025-01-21
Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.
BMC genomics, 26(1):51.
BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.
RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.
CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.
Additional Links: PMID-39833680
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Citation:
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@article {pmid39833680,
year = {2025},
author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M},
title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {51},
pmid = {39833680},
issn = {1471-2164},
mesh = {*Extreme Environments ; Genome, Bacterial ; Phylogeny ; Genomics/methods ; Ecosystem ; Adaptation, Physiological/genetics ; Metals, Heavy/toxicity ; Biodegradation, Environmental ; Soil Microbiology ; },
abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.
RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.
CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.},
}
MeSH Terms:
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*Extreme Environments
Genome, Bacterial
Phylogeny
Genomics/methods
Ecosystem
Adaptation, Physiological/genetics
Metals, Heavy/toxicity
Biodegradation, Environmental
Soil Microbiology
RevDate: 2025-01-20
Fungal Planet description sheets: 1697-1780.
Fungal systematics and evolution, 14:325-577.
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.
Additional Links: PMID-39830292
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@article {pmid39830292,
year = {2024},
author = {Crous, PW and Wingfield, MJ and Jurjević, Ž and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, Ø and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ},
title = {Fungal Planet description sheets: 1697-1780.},
journal = {Fungal systematics and evolution},
volume = {14},
number = {},
pages = {325-577},
doi = {10.3114/fuse.2024.14.19},
pmid = {39830292},
issn = {2589-3831},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.},
}
RevDate: 2025-01-19
CmpDate: 2025-01-19
Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.
Microbial ecology, 87(1):173.
Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.
Additional Links: PMID-39828718
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Citation:
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@article {pmid39828718,
year = {2025},
author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X},
title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {173},
pmid = {39828718},
issn = {1432-184X},
support = {41976131//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; China ; *Bacteria/classification/genetics/isolation & purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; Ecosystem ; Metals, Heavy/analysis ; },
abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.},
}
MeSH Terms:
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hide MeSH Terms
*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
China
*Bacteria/classification/genetics/isolation & purification
*Estuaries
*Rivers/microbiology
*Microbiota
Biodiversity
Ecosystem
Metals, Heavy/analysis
RevDate: 2025-01-18
Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.
Journal of hazardous materials, 487:137241 pii:S0304-3894(25)00153-0 [Epub ahead of print].
How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.
Additional Links: PMID-39826456
Publisher:
PubMed:
Citation:
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@article {pmid39826456,
year = {2025},
author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T},
title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137241},
doi = {10.1016/j.jhazmat.2025.137241},
pmid = {39826456},
issn = {1873-3336},
abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.},
}
RevDate: 2025-01-18
CmpDate: 2025-01-18
From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.
Gut microbes, 17(1):2452277.
The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.
Additional Links: PMID-39826104
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PubMed:
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@article {pmid39826104,
year = {2025},
author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P},
title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2452277},
doi = {10.1080/19490976.2025.2452277},
pmid = {39826104},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/microbiology ; Animals ; Immunotherapy/methods ; Tumor Microenvironment/drug effects ; Treatment Outcome ; Combined Modality Therapy ; },
abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.},
}
MeSH Terms:
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hide MeSH Terms
Humans
*Fecal Microbiota Transplantation
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Microbiome
*Neoplasms/therapy/microbiology
Animals
Immunotherapy/methods
Tumor Microenvironment/drug effects
Treatment Outcome
Combined Modality Therapy
RevDate: 2025-01-18
CmpDate: 2025-01-18
The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.
Environmental microbiology, 27(1):e70022.
Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.
Additional Links: PMID-39825576
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PubMed:
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@article {pmid39825576,
year = {2025},
author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA},
title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70022},
doi = {10.1111/1462-2920.70022},
pmid = {39825576},
issn = {1462-2920},
mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Soil Microbiology
Animals
*Microbiota
*Herbivory
*Grassland
*Bacteria/classification/genetics/metabolism
*RNA, Ribosomal, 16S/genetics
Soil/chemistry
Carbon/metabolism
RevDate: 2025-01-17
CmpDate: 2025-01-17
Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.
BMC microbiology, 25(1):27.
Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.
Additional Links: PMID-39825218
PubMed:
Citation:
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@article {pmid39825218,
year = {2025},
author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM},
title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {27},
pmid = {39825218},
issn = {1471-2180},
support = {2021/10626-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/05561-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 01.02.016301.00293/2021//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; },
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; },
abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Soil Microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Plant Roots/microbiology
Brazil
*Poaceae/microbiology
Soil/chemistry
RNA, Ribosomal, 16S/genetics
Rainforest
Biodiversity
RevDate: 2025-01-17
CmpDate: 2025-01-17
A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.
Drug development research, 86(1):e70045.
Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.
Additional Links: PMID-39821365
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@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics & numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Famotidine/adverse effects
*Adverse Drug Reaction Reporting Systems/statistics & numerical data
United States/epidemiology
*Histamine H2 Antagonists/adverse effects
*Pharmacovigilance
*United States Food and Drug Administration
Female
Male
Adult
Middle Aged
Aged
Adolescent
Young Adult
Child
Child, Preschool
Drug-Related Side Effects and Adverse Reactions/epidemiology
Databases, Factual
Infant
RevDate: 2025-01-17
CmpDate: 2025-01-17
Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.
Microbial ecology, 87(1):171.
The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.
Additional Links: PMID-39820572
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Citation:
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@article {pmid39820572,
year = {2025},
author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I},
title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {171},
pmid = {39820572},
issn = {1432-184X},
support = {US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; IT1678-22//Eusko Jaurlaritza/ ; },
mesh = {*Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Spain ; *RNA, Ribosomal, 16S/genetics ; *Salinity ; *Microbiota ; *Biodiversity ; Phylogeny ; Natural Springs/microbiology ; Water Microbiology ; },
abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Bacteria/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Spain
*RNA, Ribosomal, 16S/genetics
*Salinity
*Microbiota
*Biodiversity
Phylogeny
Natural Springs/microbiology
Water Microbiology
RevDate: 2025-01-17
CmpDate: 2025-01-17
Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.
Microbial ecology, 87(1):172.
Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.
Additional Links: PMID-39820498
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Citation:
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@article {pmid39820498,
year = {2025},
author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z},
title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {172},
pmid = {39820498},
issn = {1432-184X},
support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; },
mesh = {*Wetlands ; *Estuaries ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Soil Microbiology ; Ecosystem ; Drug Resistance, Microbial/genetics ; Geologic Sediments/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Wetlands
*Estuaries
*Bacteria/genetics/classification/drug effects/isolation & purification
Soil Microbiology
Ecosystem
Drug Resistance, Microbial/genetics
Geologic Sediments/microbiology
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Water Microbiology
Drug Resistance, Bacterial/genetics
RevDate: 2025-01-17
Editorial FEMS EC Thematic Issue Aquatic Microbial Ecology.
FEMS microbiology ecology pii:7958962 [Epub ahead of print].
Additional Links: PMID-39820407
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PubMed:
Citation:
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@article {pmid39820407,
year = {2025},
author = {Hahn, MW and Kisand, V},
title = {Editorial FEMS EC Thematic Issue Aquatic Microbial Ecology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf005},
pmid = {39820407},
issn = {1574-6941},
}
RevDate: 2025-01-16
Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.
Applied and environmental microbiology [Epub ahead of print].
Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.
Additional Links: PMID-39817738
Publisher:
PubMed:
Citation:
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@article {pmid39817738,
year = {2025},
author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL},
title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0206924},
doi = {10.1128/aem.02069-24},
pmid = {39817738},
issn = {1098-5336},
abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.},
}
RevDate: 2025-01-15
Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.
Environmental science & technology [Epub ahead of print].
Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.
Additional Links: PMID-39813101
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PubMed:
Citation:
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@article {pmid39813101,
year = {2025},
author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y},
title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07954},
pmid = {39813101},
issn = {1520-5851},
abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.},
}
RevDate: 2025-01-15
Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.
Heliyon, 11(1):e41400.
Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.
Additional Links: PMID-39811355
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@article {pmid39811355,
year = {2025},
author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS},
title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.},
journal = {Heliyon},
volume = {11},
number = {1},
pages = {e41400},
pmid = {39811355},
issn = {2405-8440},
abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.},
}
RevDate: 2025-01-14
CmpDate: 2025-01-14
Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.
FEMS microbiology ecology, 101(1):.
The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.
Additional Links: PMID-39808188
Publisher:
PubMed:
Citation:
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@article {pmid39808188,
year = {2025},
author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM},
title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {1},
pages = {},
doi = {10.1093/femsec/fiae168},
pmid = {39808188},
issn = {1574-6941},
support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; },
mesh = {*Fruit/microbiology ; *Vaccinium myrtillus/microbiology ; *Endophytes/genetics/isolation & purification/classification/metabolism ; *Fungi/genetics/classification/isolation & purification/growth & development ; *Phenols/metabolism ; *Mycobiome ; },
abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.},
}
MeSH Terms:
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*Fruit/microbiology
*Vaccinium myrtillus/microbiology
*Endophytes/genetics/isolation & purification/classification/metabolism
*Fungi/genetics/classification/isolation & purification/growth & development
*Phenols/metabolism
*Mycobiome
RevDate: 2025-01-14
phylotypr: an R package for classifying DNA sequences.
Microbiology resource announcements [Epub ahead of print].
The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.
Additional Links: PMID-39807875
Publisher:
PubMed:
Citation:
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@article {pmid39807875,
year = {2025},
author = {Schloss, PD},
title = {phylotypr: an R package for classifying DNA sequences.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0114424},
doi = {10.1128/mra.01144-24},
pmid = {39807875},
issn = {2576-098X},
abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.},
}
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