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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 09 Apr 2020 at 01:45 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: 2020-04-08

Compte-Port S, Fillol M, Gich F, et al (2020)

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources.

PloS one, 15(4):e0231238 pii:PONE-D-19-33592.

Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.

RevDate: 2020-04-08

Altermann E, WJ Hickey (2020)

Grand Challenges in Microbiotechnology: Through the Prism of Microbiotechnology.

Frontiers in microbiology, 11:430.

RevDate: 2020-04-08

Chen Z, Xie Y, Zhou F, et al (2020)

Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease.

Frontiers in microbiology, 11:383.

Dysbiosis of gut microbiota during the progression of HBV-related liver disease is not well understood, as there are very few reports that discuss the featured bacterial taxa in different stages. The aim of this study was to reveal the featured bacterial species whose abundances are directly associated with HBV disease progression, that is, progression from healthy subjects to, chronic HBV infection, chronic hepatitis B to liver cirrhosis. Approximately 400 fecal samples were collected, and 97 samples were subjected to 16S rRNA gene sequencing after age and BMI matching. Compared with the healthy individuals, significant gut microbiota alterations were associated with the progression of liver disease. LEfSe results showed that the HBV infected patients had higher Fusobacteria, Veillonella, and Haemophilus abundance while the healthy individuals had higher levels of Prevotella and Phascolarctobacterium. Indicator analysis revealed that 57 OTUs changed as the disease progressed, and their combination produced an AUC value of 90% (95% CI: 86-94%) between the LC and non-LC groups. In addition, the abundances of OTU51 (Dialister succinatiphilus) and OTU50 (Alistipes onderdonkii) decreased as the disease progressed, and these results were further verified by qPCR. The LC patients had the higher bacterial network complexity, which was accompanied with a lower abundance of potential beneficial bacterial taxa, such as Dialister and Alistipes, while they had a higher abundance of pathogenic species within Actinobacteria. The compositional and network changes in the gut microbiota in varied CHB stages, suggest the potential contributions of gut microbiota in CHB disease progression.

RevDate: 2020-04-08

Zehentner B, Ardern Z, Kreitmeier M, et al (2020)

A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC).

Frontiers in microbiology, 11:377.

Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. An active σ70 promoter, transcription start site (TSS), Shine-Dalgarno motif and rho-independent terminator were experimentally validated, providing evidence that this open reading frame has all the structural features of a functional gene. Furthermore, ribosomal profiling revealed translation of the mRNA, the protein was detected in Western blots and a pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene), thus adding another example to the growing list of overlapping, protein coding genes in bacteria.

RevDate: 2020-04-08

Malki K, Rosario K, Sawaya NA, et al (2020)

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.

mBio, 11(2): pii:mBio.00436-20.

Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml-1 to 1.1 × 105 ml-1 and 2.2 × 103 ml-1 to 3.4 × 104 ml-1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.

RevDate: 2020-04-07

Gizaw F, Kekeba T, Teshome F, et al (2020)

Distribution and antimicrobial resistance profile of coagulase-negative staphylococci from cattle, equipment, and personnel on dairy farm and abattoir settings.

Heliyon, 6(3):e03606 pii:e03606.

Background: Safe food is central to social wellbeing. Coagulase-negative staphylococci (CNS) are a threat to food safety because they may harbor multiple enterotoxins and antimicrobial resistance (AMR) genes. CNS bacteria are an emerging nosocomial pathogen in public health. CNS also cause bovine mastitis with a significant economic loss in the dairy industry and may introduce toxins to the food supply chain resulting in foodborne illnesses. However, information on CNS and their AMR status are scarce in food animal production and processing lines in Ethiopia.

Methodology: This cross-sectional study evaluated the prevalence and AMR patterns of CNS in dairy farms and abattoirs using samples (n = 1001) from udder milk, beef carcass, personnel, and different abattoir and dairy equipment across five locations of central Oromia. The CNS isolates were identified via standard microbiological protocols and evaluated using disc diffusion test against 14 antimicrobials belonging to nine different broad classes. Uni-and-multivariable logistic regressions were used to analyze the association between potential risk factors (location, sample source, and sample type) and positivity to CNS.

Results: The overall prevalence of CNS in the five different geographic locations studied was 9.6% (range: 6.7-12.4%) and varied between abattoirs (11.3%) and dairy farms (8.0%). CNS were prevalent on the carcass, milk, equipment, personnel hands, and nasal samples. Of all CNS isolates, 7.1, 10.7, 7.1, 12.5, 17.9, 10.7, 12.5, 7.1, 1.8, 5.4, 1.8, and 5.4% exhibited AMR simultaneously to single, double, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, and 13 antimicrobials, respectively. Overall, the isolates displayed 51 different AMR phenotypic patterns in which 50% of the isolates exhibited quadruple-resistance simultaneously based on the nine broad antimicrobial classes tested using 14 representative antimicrobials. The prevalence of multidrug-resistant (MDR) CNS (i.e. ≥ 3 classes of antimicrobials) was significantly (p = 0.037) different between locations with 100, 57.1, 50, 86.7, and 76.9% in Addis Ababa, Adama, Assela, Bishoftu, and Holeta, respectively. However, the prevalence of MDR CNS was not significantly (p = 0.20) different between dairy farms (87.5%) and abattoirs (71.9%). We evaluated the effect of acquiring cefoxitin-resistance of the isolates on the efficacy (i.e. inhibition zone) of the rest antimicrobials using General Linear Model after adjusting geographical locations as a random effect. Isolates with cefoxitin-resistance significantly displayed resistance to eight antimicrobials of 14 tested including amoxicillin, penicillin, cloxacillin, chloramphenicol, nalidixic acid, nitrofurantoin, and tetracycline (p = 0.000), and erythromycin (p = 0.02). On the other hand, cefoxitin-resistant isolates were susceptible to gentamicin, ciprofloxacin, kanamycin, streptomycin, and sulphamethoxazone trimethoprim (p = 0.000). Thus, antimicrobials such as gentamicin and ciprofloxacin may be an alternative therapy to treat cefoxitin-resistant CNS, as 96.4% of CNS isolates were susceptible to these antimicrobials. Overall, 94.1 and 54.5% of the CNS isolates among cefoxitin-resistant and cefoxitin-susceptible, respectively, harbored resistance to 3 or more classes of antimicrobials i.e. MDR.

Conclusion: The overall prevalence of CNS in milk, meat, equipment, and food handlers in central Oromia was 9.6% but varied by location and sample source. Some specific niches such as equipment, hands, and nasal cavities of personnel are significant sites for the source of CNS. Most, but not all, MDR CNS isolates were cefoxitin-resistant. Overall, 78.6% of the CNS tested were MDR and 50% had resistance to four or more broad classes of antimicrobials. CNS in food animals (raw milk and meat), equipment, and food handlers can be the source of MDR to the public. Personnel safety and hygienic food handling practices are needed. In addition, further investigation into the risk factors for the transmission and mechanisms of resistance of the CNS is required for intervention.

RevDate: 2020-04-07

Redmile-Gordon M, Gregory AS, White RP, et al (2020)

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use.

Geoderma, 363:114143.

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R2 = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.

RevDate: 2020-04-07

Nisenbaum M, Corti-Monzón G, Villegas-Plazas M, et al (2020)

Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters.

Biodegradation pii:10.1007/s10532-020-09896-w [Epub ahead of print].

Oily bilge wastewater (OBW) is a hazardous hydrocarbon-waste generated by ships worldwide. In this research, we enriched, characterized and study the hydrocarbon biodegradation potential of a microbial consortium from the bilges of maritime ships. The consortium cZ presented a biodegradation efficiency of 66.65% for total petroleum hydrocarbons, 72.33% for aromatics and 97.76% removal of n-alkanes. This consortium showed the ability to grow in OBWs of diverse origin and concentration. A 67-fold increase in biomass was achieved using a Sequential Batch Reactor with OBW as the only carbon and energy source. The bacterial community composition of the enriched OBW bacterial consortium at the final stable stage was characterized by 16S amplicon Illumina sequencing showing that 25 out of 915 of the emerged predominant bacterial types detected summed up for 84% of total composition. Out of the 140 taxa detected, 13 alone accumulated 94.9% of the reads and were classified as Marinobacter, Alcanivorax, Parvibaculum, Flavobacteriaceae, Gammaproteobacteria PYR10d3, Novispirillum and Xanthomonadaceae among the most predominant, followed by Thalassospira, Shewanella, Rhodospirillaceae, Gammaprotobacteria, Rhodobacteriaceae and Achromobacter. The microbial community from OBW bioreactor enrichments is intrinsically diverse with clear selection of predominant types and remarkably exhibiting consistent and efficient biodegradation achieved without any nutrient or surfactant addition. Due to there is very little information available in the OBW biodegradation field, this work contributes to the body of knowledge surrounding the treatment improvement of this toxic waste and its potential application in wastewater management.

RevDate: 2020-04-06

Tian Z, Wang T, Tunlid A, et al (2020)

Proteolysis of Iron Oxide-Associated Bovine Serum Albumin.

Environmental science & technology [Epub ahead of print].

Proteins are a substantial nitrogen source in soils provided that they can be hydrolyzed into bioavailable small peptides or amino acids. However, the strong associations between proteins and soil minerals restrict such proteolytic reactions. This study focused on how an extracellular fungal protease (Rhizopus sp.) hydrolyzed iron oxide-associated bovine serum albumin (BSA) and the factors that affected the proteolysis. We combined batch experiments with size-exclusion and reversed phase liquid chromatography and in situ infrared spectroscopic measurements to monitor the generation of proteolytic products in solution as well as the real-time changes of the adsorbed BSA during 24 h. Results showed that protease hydrolyzed the iron oxide-associated BSA directly at the surface without an initial desorption of BSA. Concurrently, the protease was adsorbed to vacant surface sites at the iron oxides, which significantly slowed down the rate of proteolysis. This inhibiting effect was counteracted by the presence of preadsorbed phosphate or by increasing the BSA coverage, which prevented protease adsorption. Fast initial rates of iron oxide-associated BSA proteolysis, comparable to proteolysis of BSA in solution, and very slow rates at prolonged proteolysis suggest a large variability in mineral-associated proteins as a nitrogen source in soils and that only a fraction of the protein is bioavailable.

RevDate: 2020-04-05

Huang S, Kleerebezem R, Rabaey K, et al (2020)

Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10551-w [Epub ahead of print].

Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day-1, with a concurrent production of n-butyrate of 7.9 mM day-1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

RevDate: 2020-04-05

Kalaimurugan D, Durairaj K, Kumar AJ, et al (2020)

Novel preparation of fungal conidiophores biomass as adsorbent for removal of phosphorus from aqueous solution.

Environmental science and pollution research international pii:10.1007/s11356-020-08307-0 [Epub ahead of print].

The present study focused on phosphorus adsorption by novel fungal conidiophores biomass in aqueous solution. Fungal Conidiophores biomass was prepared from the fungal strains Aspergillus oryzae (YFK) and Fusarium oxysporum (YVS2). The functional groups and morphology of Conidiophores Biomass (CB) from these strains were characterized by FTIR and SEM. FTIR confirms the presence of alcohol, carboxylic acid, carbon dioxide, cyclic alkene, amine, alkene, fluoro compound, and halo compound groups. Batch mode study was carried out with two CB's such as Aspergillus oryzae CB (ACB) and Fusarium oxysporum CB (FCB) with initial concentration of phosphorus ranging from 20 to 100 mg L-1. Based on the batch experiments, the adsorption kinetics (pseudo first order and pseudo second order), isotherms (Freundlich and Langmuir models), and thermodynamic (standard entropy, energy, and enthalpy) parameters were calculated. The adsorption kinetics and isotherm studies showed that the adsorption data well fitted with PSO kinetic model. From the isotherm results, it was found that ACB and FCB exhibited highest adsorption capacity 25.64 mg g-1 and 26.32 mg g-1 of phosphorus respectively at the optimal condition of pH (7), time (90 min), dose (250 mg), and room temperature (35 °C). Thermodynamics values were found to be endothermic and spontaneous in nature for phosphorus adsorption. Finally, the results suggested that the ACB and FCB are economically feasible cost-effective adsorbent for removal of phosphorus in wastewater treatment. Graphical abstract.

RevDate: 2020-04-05

Chique C, Hynds PD, Andrade L, et al (2020)

Cryptosporidium spp. in groundwater supplies intended for human consumption - A descriptive review of global prevalence, risk factors and knowledge gaps.

Water research, 176:115726 pii:S0043-1354(20)30263-3 [Epub ahead of print].

Cryptosporidiosis is one of the leading causes of diarrhoeal illness and mortality induced by protozoan pathogens worldwide. As a largely waterborne disease, emphasis has been given to the study of Cryptosporidium spp. in surface waters, readily susceptible to pathogenic contamination. Conversely, the status of Cryptosporidium in potable groundwater sources, generally regarded as a pristine and "safe" drinking-water supply owing to (sub)-soil protection, remains largely unknown. As such, this investigation presents the first literature review aimed to ascertain the global prevalence of Cryptosporidium in groundwater supply sources intended for human consumption. Thirty-seven peer-reviewed studies were identified and included in the review. Groundwater sample and supply detection rates (estimated 10-20%) indicate Cryptosporidium is frequently present in domestic groundwater sources, representing a latent health concern for groundwater consumers. Specifically, sample (10.4%) and source (19.1%) detection rates deriving from comprehensive "temporal" investigations are put forward as representative of a contamination 'baseline' for Cryptosporidium in 'domestic' groundwater supplies. Proposed 'baseline' prevalence figures are largely applicable in preventive risk-based catchment and groundwater quality management including the formulation of Quantitative Microbial Risk Assessment (QMRA). Notwithstanding, a large geographical disparity in available investigations and lack of standardized reporting restrict the transferability of research findings. Overall, the mechanisms responsible for Cryptosporidium transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between groundwater and public-health sub-disciplines among investigations. Key recommendations and guidelines are provided for prospective studies directed at more integrative and multi-disciplinary research.

RevDate: 2020-04-05

Jin D, Zhang F, Shi Y, et al (2020)

Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation.

Environmental research, 185:109457 pii:S0013-9351(20)30350-9 [Epub ahead of print].

Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.

RevDate: 2020-04-04

Chen YC, Li Z, Zhao YX, et al (2020)

The Litsea genome and the evolution of the laurel family.

Nature communications, 11(1):1675 pii:10.1038/s41467-020-15493-5.

The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.

RevDate: 2020-04-03

Heys C, Cheaib B, Busetti A, et al (2020)

Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.

Applied and environmental microbiology, 86(8): pii:AEM.02283-19.

In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

RevDate: 2020-04-03

Nelson CW, Ardern Z, X Wei (2020)

OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.

Molecular biology and evolution pii:5815567 [Epub ahead of print].

Purifying (negative) natural selection is a hallmark of functional biological sequences, and can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous substitutions per site (dN/dS). However, when two genes overlap the same nucleotide sites in different frames, synonymous changes in one gene may be nonsynonymous in the other, perturbing dN/dS. Thus, scalable methods are needed to estimate functional constraint specifically for overlapping genes (OLGs). We propose OLGenie, which implements a modification of the Wei-Zhang method. Assessment with simulations and controls from viral genomes (58 OLGs and 176 non-OLGs) demonstrates low false positive rates and good discriminatory ability in differentiating true OLGs from non-OLGs. We also apply OLGenie to the unresolved case of HIV-1's putative antisense protein gene, showing significant purifying selection. OLGenie can be used to study known OLGs and to predict new OLGs in genome annotation. Software and example data are freely available at https://github.com/chasewnelson/OLGenie.

RevDate: 2020-04-02

Zhang JQ, Zhou T, Guo LP, et al (2020)

[Ecological benefits of Gastrodia elata-Phallus impudicus sequential planting pattern].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 45(3):457-462.

Gastrodia elata is a kind of precious traditional Chinese medicine. In the process of cultivation of G. elata, due to the influence of continuous cropping obstacles and other factors, the fungus materials and land that have been planted with G. elata are often abandoned, resulting in a great waste of resources. Based on the planting characteristics of G. elata and Phallus impudicus and the previous research experience in ecological agriculture, this paper analyzed the ecological adaptability characteristics of G. elata and P. impudicus, and summarized the key techniques of the G. elata-P. impudicus sequential planting pattern. Keeping track of the planting area, fungus-growing materials consumption and market sales of G. elata-P. impudicus sequential planting pattern, the ecological benefits of G. elata-P. impudicus sequential planting pattern from the aspects of utilization rate of fungus-growing materials were analyzed, the value of land resources per unit area, ecological environmental protection, labor cost and economic benefits were consi-dered. The technical principle of G. elata-P. impudicus sequential planting pattern was expounded according to their ecological habit, the season of harvest and planting, the difference of composition of fungus-growing materials, and the microbial ecology. The sequential planting pattern of G. elata-P. impudicus not only realized the double production of medicinal materials and edible fungi, reduced the waste of old fungus-growing materials, but also transformed the energy from nutrition-supplied fungi to edible and medicinal fungi, which guaranteed the ecological recycling and utilization of G. elata in the process of cultivation.

RevDate: 2020-04-02

Silveira-Nunes G, Durso DF, Jr LRAO, et al (2020)

Hypertension Is Associated With Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population.

Frontiers in pharmacology, 11:258.

Hypertension is a major global health challenge, as it represents the main risk factor for stroke and cardiovascular disease. It is a multifactorial clinical condition characterized by high and sustained levels of blood pressure, likely resulting from a complex interplay of endogenous and environmental factors. The gut microbiota has been strongly supposed to be involved but its role in hypertension is still poorly understood. In an attempt to fill this gap, here we characterized the microbial composition of fecal samples from 48 hypertensive and 32 normotensive Brazilian individuals by next-generation sequencing of the 16S rRNA gene. In addition, the cytokine production of peripheral blood samples was investigated to build an immunological profile of these individuals. We identified a dysbiosis of the intestinal microbiota in hypertensive subjects, featured by reduced biodiversity and distinct bacterial signatures compared with the normotensive counterpart. Along with a reduction in Bacteroidetes members, hypertensive individuals were indeed mainly characterized by increased proportions of Lactobacillus and Akkermansia while decreased relative abundances of well-known butyrate-producing commensals, including Roseburia and Faecalibacterium within the Lachnospiraceae and Ruminococcaceae families. We also observed an inflamed immune profile in hypertensive individuals with an increase in TNF/IFN-γ ratio, and in TNF and IL-6 production when compared to normotensive ones. Our work provides the first evidence of association of hypertension with altered gut microbiota and inflammation in a Brazilian population. While lending support to the existence of potential microbial signatures of hypertension, likely to be robust to age and geography, our findings point to largely neglected bacteria as potential contributors to intestinal homeostasis loss and emphasize the high vulnerability of hypertensive individuals to inflammation-related disorders.

RevDate: 2020-03-31

Chen ML, Becraft ED, Pachiadaki M, et al (2020)

Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.

Frontiers in microbiology, 11:376.

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

RevDate: 2020-03-30

McAteer PG, Christine Trego A, Thorn C, et al (2020)

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater.

Bioresource technology, 307:123221 pii:S0960-8524(20)30492-2 [Epub ahead of print].

Low temperature anaerobic digestion remains in its infancy, despite increasing interest for the treatment of complex wastewaters. In this study, the feasibility of low-temperature anaerobic treatment of dairy wastewater was assessed during a 443-day laboratory-scale bioreactor trial. The bioreactors were operated in triplicate at organic loading rates of 7.5-9 kgCODm-3d-1 throughout five operational phases. The structure of the microbial community was analysed using quantitative real-time PCR and amplicon sequencing of 16S rRNA genes from DNA and rRNA. The results indicated that low-temperature treatment of dairy wastewater is feasible at 15 °C, but that reactor configuration remains extremely important. The upflow anaerobic sludge bed (UASB) configuration out-performed the expanded granular sludge bed (EGSB)-based configurations. Decreased temperatures resulted in significant reductions in microbiome diversity. Methanosaeta was identified as a dominant genus throughout the trial, while Lactococcus was identified as an important bacterial genus at low-temperatures. However, the relative abundance of Lactococcus was significantly influenced by reactor configuration.

RevDate: 2020-03-29

Núñez A, DA Moreno (2020)

The Differential Vertical Distribution of the Airborne Biological Particles Reveals an Atmospheric Reservoir of Microbial Pathogens and Aeroallergens.

Microbial ecology pii:10.1007/s00248-020-01505-w [Epub ahead of print].

The most abundant biological particles present in the air are bacteria, fungal propagules and pollen grains. Many of them are proved allergens or even responsible for airborne infectious diseases, which supports the increase of studies in recent years on their composition, diversity, and factors involved in their variability. However, most studies in urban areas are conducted close to ground level and a factor such as height is rarely taken into account. Thus, the information about how the composition of biological particles changes with this variable is scarce. Here, we examined the differential distribution of bacteria, fungi, and plants at four altitudes (up to ∼ 250 m) in a metropolitan area using high-throughput DNA sequencing. Most taxa were present at all levels (common taxa). However, a transitional layer between 80 and 150 m seemed to affect the scattering of these bioaerosols. Taxa not present at all altitudes (non-common) showed an upward tendency of diversity for bacteria and plants with height, while the opposite trend was observed for fungi. Certain patterns were observed for fungi and specific plant genera, while bacterial taxa showed a more arbitrary distribution and no patterns were found. We detected a wide variety of aeroallergens and potential pathogens at all heights, which summed a substantial portion of the total abundance for fungi and plants. We also identified potential connections between the biological particles based on their abundances across the vertical section.

RevDate: 2020-03-29

Wu R, Chai B, Cole JR, et al (2020)

Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.

The ISME journal pii:10.1038/s41396-020-0635-1 [Epub ahead of print].

There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

RevDate: 2020-03-29

Sims IM, GW Tannock (2020)

Utilization of galacto- and fructo-oligosaccharides for growth by co-cultures of bifidobacterial species characteristic of the infant gut.

Applied and environmental microbiology pii:AEM.00214-20 [Epub ahead of print].

Bifidobacterial species are common inhabitants of the gut of human infants during the period when milk is a major component of the diet. Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subspecies longum, and B. longum subspecies infantis have been detected frequently in infant feces, but subsp. infantis may be disadvantaged numerically in the gut of infants in westernized countries. This may be due to the different durations of breast milk feeding in different countries. Supplementation of the infant diet or replacement of breast milk using formula feeds is common in western countries. Formula milks often contain galacto- and/or fructo-oligosaccharides ('GOS', 'FOS', respectively) as additives to augment the concentration of oligosaccharides in ruminant milks, but the ability of subsp. infantis to utilize these potential growth substrates when in competition with other bifidobacterial species is unknown. We compared the growth and oligosaccharide utilization of GOS and FOS by bifidobacterial species in pure and co-culture. Short chain GOS and FOS (degree of polymerization [DP] 2 and 3) were favored growth substrates for strains of B. bifidum and B. longum subsp. longum, whereas both B. breve and B. longum subsp. infantis had ability to utilize both short and longer chain GOS and FOS (DP 2-6). B. breve was nevertheless numerically dominant over subsp. infantis in co-cultures. This was probably related to the slower use of GOS of DP3 by subsp. infantis, indicating that the kinetics of substrate utilization is an important ecological factor in the assemblage of gut communities.Importance The kinds of bacteria that form the collection of microbes (the microbiota) in the gut of human infants may influence health and well-being. Knowledge of how the composition of the infant diet influences the assemblage of the bacterial collection is therefore important because dietary interventions may offer opportunities to alter the microbiota with the aim of improving health. Bifidobacterium longum subspecies infantis is a well-known bacterial species, but under modern child-rearing conditions it may be disadvantaged in the gut. Modern formula milks often contain particular oligosaccharide additives that are generally considered to support bifidobacterial growth. However, studies of the ability of various bifidobacterial species to grow together while using these oligosaccharides have not been conducted. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of human nutrition on the development of the gut microbiota.

RevDate: 2020-03-29

Belleggia L, Milanović V, Ferrocino I, et al (2020)

Is there any still undisclosed biodiversity in Ciauscolo salami? A new glance into the microbiota of an artisan production as revealed by high-throughput sequencing.

Meat science, 165:108128 pii:S0309-1740(19)31181-7 [Epub ahead of print].

Ciauscolo is a fermented sausage with the Protected Geographical Indication (PGI) status. To disclose the microbial ecology of a model Ciauscolo salami manufacture during its natural fermentation, viable counting, amplicon-based sequencing and real-time PCR were applied. The volatilome during fermentation was also characterized. The results allowed previously undetected species to be discovered. The core microbiota was composed by Lactobacillus algidus, Leuconostoc carnosum, Lactobacillus sakei, Debaryomyces hansenii, Glomus hyderabadensis, Tilletiopsis washingtonensis, and Kurtzmaniella zeylanoides. Salmonella spp. and Listeria monocytogenes were absent in all the samples; moreover, multiplex real-time PCR revealed the absence of the target genes bont/A, bont/B, bont/E, bont/F, and 4gyrB (CP), encoding botulinic toxins. Volatilome, deeply depending on microbiological metabolism, was characterized by spices-derived components. Limonene, sabinene, α- and β-pinene, 3-carene, and α-thujene were the most represented monoterpene hydrocarbons, whereas β- and α-copaene were the most represented sesquiterpene hydrocarbons. Allyl methyl sulphide and diallyl disulphide were the major aliphatic sulphur compounds, together with diallyl sulphide and allyl methyl disulphide.

RevDate: 2020-03-28

Zhengchao H, Yue S, Xianqing H, et al (2020)

Microbial diversity of representative traditional fermented sausages in different regions of China.

Journal of applied microbiology [Epub ahead of print].

AIMS: The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.

METHODS AND RESULTS: The diversity of the microbiota of the sausages were studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78.39%, 13.13% and 7.14% in SC, 35.47%, 30.36% and 28.04% in GD, 54.81%, 28.91% and 14.00% in HN, 20.20%, 58.16% and 17.31% in HB, respectively. The dominant genus distribution of fermented sausages in different regions is regions varied, however lactic acid bacteria and cyanobacteria were dominant overall. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage microorganisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.

CONCLUSIONS: The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavor of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic microorganisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavor and also improve the microbial resource utilization, and contribute to the control of harmful microorganisms in traditional fermented sausage.

RevDate: 2020-03-28

Sodhi KK, Kumar M, DK Singh (2020)

Potential application in amoxicillin removal of Alcaligenes sp. MMA and enzymatic studies through molecular docking.

Archives of microbiology pii:10.1007/s00203-020-01868-1 [Epub ahead of print].

Antibiotic contamination in environmental matrices is a serious global problem which leads to an increase in the proliferation of antibiotic resistance genes. Amoxicillin is ubiquitous in the environment, but there is hardly any information on the dissipation of amoxicillin by the microbial community. In view of this, the present study focusses on the removal of amoxicillin using amoxicillin-resistant bacteria, Alcaligenes sp. MMA. Bacteria were characterized using antibiotic tests, biochemical and molecular analysis. Alcaligenes sp. MMA was able to remove up to 84% of amoxicillin in 14 days in M9 minimal media, and the degradation products were confirmed using LC-MS/MS, including the benzothiazole, 2-Amino-3-methoxyl benzoic acid, 4-Hydroxy-2-methyl benzoic acid, 5-Amino-2-methylphenol and 3,5-Bis(tert-butyl)-2-hydroxybenzaldehyde, at the end of 14th day which further shows the removal of amoxicillin by the bacterial strain. Differential expression of porins was found in the presence of amoxicillin as a sole source of carbon and energy for the bacterial strain. Molecular interaction using in silico studies were performed which showed the formation of a hydrogen bond between amoxicillin and porins.

RevDate: 2020-03-28

Urra J, Alkorta I, Mijangos I, et al (2020)

Commercial and farm fermented liquid organic amendments to improve soil quality and lettuce yield.

Journal of environmental management, 264:110422 pii:S0301-4797(20)30356-X [Epub ahead of print].

The anaerobic decomposition of organic wastes might lead to the formation of organic-byproducts which can then be successfully used as organic fertilizers. This study evaluated the impact of the application of two fermented liquid organic amendments (commercial vs. farm-made) at two doses of application (optimal vs. suboptimal), compared to mineral fertilization, on lettuce growth and soil quality. To this purpose, two experiments were conducted at microcosm- and field-scale, respectively. In the microcosm experiment, organically amended soils resulted in lower lettuce yield than minerally fertilized soil but, in contrast, they enhanced microbial activity and biomass, thus leading to an improvement in soil quality. The fertilization regime (organic vs. inorganic) significantly affected soil microbial composition but did not have any significant effect on structural or functional prokaryotic diversity. In the field experiment, at the optimal dose of application, organically-amended soils resulted in comparable lettuce yield to that displayed by minerally fertilized soils. The application of organic amendments did not result in an enhanced microbial activity and biomass, compared to mineral fertilization, but led to a higher soil prokaryotic diversity. Among the organically-amended plots, the optimal application dose resulted in a higher lettuce yield and soil microbial activity and biomass, but led to a decline in soil prokaryotic diversity, compared to the suboptimal application dose. Our results indicate that commercial and farm-made fermented liquid organic amendments possess the potential to ameliorate soil quality while sustaining crop yield. Given the strong influence of other factors (e.g., type of soil, dose of application) on the effects exerted by such amendments on soil quality and fertility, we recommend that an exhaustive characterization of both the amendments and the recipient soils should be carried out prior to their application, in order to better ensure their potential beneficial effects.

RevDate: 2020-03-27

Ji M, Kong W, Stegen J, et al (2020)

Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils.

Environmental microbiology [Epub ahead of print].

Rare biosphere represents the majority of Earth's biodiversity and perform vital ecological functions, yet little is known about their biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in dryland grassland soils on the Tibetan Plateau. Results revealed similar biogeographical patterns of rare and abundant bacteria at both compositional and phylogenetic levels, but rare subcommunity was more heavily influenced by stochasticity (72%) than the abundant (57%). The compositional variation of rare bacteria was less explained by environmental factors (41%) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than that of the abundant (29%). The phylogeny of rare bacteria was equally explained by local factors (soil and vegetation) and geospatial distance (11.5% and 11.9%, respectively), while that of the abundant was more explained by geospatial distance (22.1%) than local factors (11.3%). Furthermore, a substantially tighter connection between the community phylogeny and composition was observed in rare (R2 = 0.65) than in abundant bacteria (R2 = 0.08). Our study provides novel insights into the assembly processes and biographical patterns of rare and abundant bacteria in dryland soils. This article is protected by copyright. All rights reserved.

RevDate: 2020-03-27

Paduano S, Marchesi I, Casali ME, et al (2020)

Characterisation of Microbial Community Associated with Different Disinfection Treatments in Hospital hot Water Networks.

International journal of environmental research and public health, 17(6): pii:ijerph17062158.

Many disinfection treatments can be adopted for controlling opportunistic pathogens in hospital water networks in order to reduce infection risk for immunocompromised patients. Each method has limits and strengths and it could determine modifications on bacterial community. The aim of our investigation was to study under real-life conditions the microbial community associated with different chemical (monochloramine, hydrogen peroxide, chlorine dioxide) and non-chemical (hyperthermia) treatments, continuously applied since many years in four hot water networks of the same hospital. Municipal cold water, untreated secondary, and treated hot water were analysed for microbiome characterization by 16S amplicon sequencing. Cold waters had a common microbial profile at genera level. The hot water bacterial profiles differed according to treatment. Our results confirm the effectiveness of disinfection strategies in our hospital for controlling potential pathogens such as Legionella, as the investigated genera containing opportunistic pathogens were absent or had relative abundances ≤1%, except for non-tuberculous mycobacteria, Sphingomonas, Ochrobactrum and Brevundimonas. Monitoring the microbial complexity of healthcare water networks through 16S amplicon sequencing is an innovative and effective approach useful for Public Health purpose in order to verify possible modifications of microbiota associated with disinfection treatments.

RevDate: 2020-03-27

Vandekerckhove TGL, Boon N, SE Vlaeminck (2020)

Pioneering on single-sludge nitrification/denitrification at 50 °C.

Chemosphere, 252:126527 pii:S0045-6535(20)30720-7 [Epub ahead of print].

Thermophilic nitrification has been proven in lab-scale bioreactors at 50 °C. The challenge is now to develop a solution for thermophilic nitrogen removal, integrating nitrification with denitrification and aerobic carbon removal. This pioneering study aimed at a single-sludge nitrification/denitrification process at 50 °C, through exposing nitrification in a step by step approach to anoxia and/or organics. Firstly, recurrent anoxia was tolerated by a nitrifying community during long-term membrane bioreactor (MBR) operation (85 days), with high ammonium oxidation efficiencies (>98%). Secondly, five organic carbon sources did not affect thermophilic ammonium and nitrite oxidation rates in three-day aerobic batch flask incubations. Moving to long-term tests with sequencing batch reactors (SBR) and MBR (>250 days), good nitrification performance was obtained at increasing COD/Ninfluent ratios (0, 0.5, 1, 2 and 3). Thirdly, combining nitrification, recurrent anoxia and presence of organic carbon resulted in a nitrogen removal efficiency of 92-100%, with a COD/Nremoved of 4.8 ± 0.6 and a nitrogen removal rate of 50 ± 14 mg N g-1 VSS d-1. Overall, this is the first proof of principle thermophilic nitrifiers can cope with redox fluctuations (aerobic/anoxic) and the aerobic or anoxic presence of organic carbon, can functionally co-exist with heterotrophs and that single-sludge nitrification/denitrification can be achieved.

RevDate: 2020-03-26

Benítez-Páez A, Gómez Del Pugar EM, López-Almela I, et al (2020)

Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening.

mSystems, 5(2): pii:5/2/e00857-19.

Cross-sectional studies conducted with obese and control subjects have suggested associations between gut microbiota alterations and obesity, but the links with specific disease phenotypes and proofs of causality are still scarce. The present study aimed to profile the gut microbiota of lean and obese children with and without insulin resistance to characterize associations with specific obesity-related complications and understand the role played in metabolic inflammation. Through massive sequencing of 16S rRNA gene amplicons and data analysis using a novel permutation approach, we have detected decreased incidence of Blautia species, especially Blautia luti and B. wexlerae, in the gut microbiota of obese children, which was even more pronounced in cases with both obesity and insulin resistance. There was also a parallel increase in proinflammatory cytokines and chemokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and monocyte chemoattractant protein 1 [MCP-1]) in feces of obese children compared to those of lean ones. B. luti and B. wexlerae were also shown to exert an anti-inflammatory effect in peripheral blood mononuclear cell cultures in vitro, compared to non-obesity-associated species. We suggest that the depletion of B. luti and B. wexlerae species in the gut ecosystem may occur in cases of obesity and contribute to metabolic inflammation leading to insulin resistance.IMPORTANCE Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin resistance in obese individuals. Our results also indicate that these bacterial species might help to reduce inflammation causally linked to obesity-related complications. Childhood is considered a window of opportunity to tackle obesity. These new findings provide, therefore, valuable information for the future design of microbiota-based strategies for the early prevention of obesity-related complications.

RevDate: 2020-03-26

Rampelli S, Soverini M, D'Amico F, et al (2020)

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.

mSystems, 5(2): pii:5/2/e00124-20.

The gut microbiome of long-lived people display an increasing abundance of subdominant species, as well as a rearrangement in health-associated bacteria, but less is known about microbiome functions. In order to disentangle the contribution of the gut microbiome to the complex trait of human longevity, we here describe the metagenomic change of the human gut microbiome along with aging in subjects with up to extreme longevity, including centenarians (aged 99 to 104 years) and semisupercentenarians (aged 105 to 109 years), i.e., demographically very uncommon subjects who reach the extreme limit of the human life span. According to our findings, the gut microbiome of centenarians and semisupercentenarians is more suited for xenobiotic degradation and shows a rearrangement in metabolic pathways related to carbohydrate, amino acid, and lipid metabolism. Collectively, our data go beyond the relationship between intestinal bacteria and physiological changes that occur with aging by detailing the shifts in the potential metagenomic functions of the gut microbiome of centenarians and semisupercentenarians as a response to progressive dietary and lifestyle modifications.IMPORTANCE The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive health. Here, we performed a metagenomic assessment of fecal samples from semisupercentenarians, i.e., 105 to 109 years old, in comparison to young adults, the elderly, and centenarians, shedding light on the longest compositional and functional trajectory of the human gut microbiome with aging. In addition to providing a fine taxonomic resolution down to the species level, our study emphasizes the progressive age-related increase in degradation pathways of pervasive xenobiotics in Western societies, possibly as a result of a supportive process within the molecular continuum characterizing aging.

RevDate: 2020-03-26

Wilbert SA, Mark Welch JL, GG Borisy (2020)

Spatial Ecology of the Human Tongue Dorsum Microbiome.

Cell reports, 30(12):4003-4015.e3.

A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. A test bed for examining this question is the tongue dorsum, which harbors a complex and important microbial community. Here, we use multiplexed fluorescence spectral imaging to investigate the organization of the tongue microbiome at micron to hundred-micron scales. We design oligonucleotide probes for taxa both abundant and prevalent, as determined by sequence analysis. Imaging reveals a highly structured spatial organization of microbial consortia, ranging in linear dimension from tens to hundreds of microns. The consortia appear to develop from a core of epithelial cells, with taxa clustering in domains suggestive of clonal expansion. Quantitative proximity analysis provides the basis for a model of tongue dorsum microbiome organization and dynamics. Our work illustrates how high-resolution analysis of micron-scale organization provides insights into physiological functions and microbiome-host interactions.

RevDate: 2020-03-25

Marsland R, Cui W, Goldford J, et al (2020)

The Community Simulator: A Python package for microbial ecology.

PloS one, 15(3):e0230430 pii:PONE-D-19-32186.

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.

RevDate: 2020-03-24

Mehta O, Ghosh TS, Kothidar A, et al (2020)

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.

Microbial ecology pii:10.1007/s00248-020-01501-0 [Epub ahead of print].

The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.

RevDate: 2020-03-23

Botterweg-Paredes E, Blaakmeer A, Hong SY, et al (2020)

Light affects tissue patterning of the hypocotyl in the shade-avoidance response.

PLoS genetics, 16(3):e1008678 pii:PGENETICS-D-19-01478 [Epub ahead of print].

Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.

RevDate: 2020-03-23

Kamagata Y (2020)

Recent Biofilm Studies Open a New Door in Microbial Ecology.

Microbes and environments, 35(1):.

RevDate: 2020-03-23

Castledine M, Sierocinski P, Padfield D, et al (2020)

Community coalescence: an eco-evolutionary perspective.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190252.

Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

VanInsberghe D, Arevalo P, Chien D, et al (2020)

How can microbial population genomics inform community ecology?.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190253.

Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Prosser JI (2020)

Putting science back into microbial ecology: a question of approach.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190240.

Microbial ecology, the scientific study of interactions between natural microbial communities and their environments, has been facilitated by the application of molecular and 'omics'-based techniques that overcome some of the limitations of cultivation-based studies. This has increased emphasis on community ecology and 'microbiome' studies, but the majority address technical, rather than scientific challenges. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses. The term 'hypothesis' is increasingly misused and critical testing of ideas or theory is restricted to a small minority of studies. This article discusses current microbial ecology research within the context of four approaches: description, induction, inference to the best explanation and deduction. The first three of these do not follow the established scientific method and are not based on scientific ecological questions. Observations are made and sometimes compared with published data, sometimes with attempts to explain findings in the context of existing ideas or hypotheses, but all lack objectivity and are biased by the observations made. By contrast, deductive studies address ecological questions and attempt to explain currently unexplained phenomena through the construction of hypotheses, from mechanism-based assumptions, that generate predictions that are then tested experimentally. Identification of key scientific questions, research driven by meaningful hypotheses and adoption of scientific method are essential for progress in microbial ecology, rather than the current emphasis on descriptive approaches that address only technical challenges. It is, therefore, imperative that we carefully consider and define the fundamental scientific questions that drive our own research and focus on ideas, concepts and hypotheses that can increase understanding, and only then consider which techniques are required for experimental testing. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Pascual-García A, Bonhoeffer S, T Bell (2020)

Metabolically cohesive microbial consortia and ecosystem functioning.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190245.

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Ciccarese D, Zuidema A, Merlo V, et al (2020)

Interaction-dependent effects of surface structure on microbial spatial self-organization.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190246.

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Locey KJ, Muscarella ME, Larsen ML, et al (2020)

Dormancy dampens the microbial distance-decay relationship.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190243.

Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of 'seed banks'. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 106 simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Morris A, Meyer K, B Bohannan (2020)

Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190244.

Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities 'map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping in organisms. We identify two insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of searching 'agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Sorensen JW, A Shade (2020)

Dormancy dynamics and dispersal contribute to soil microbiome resilience.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190255.

In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-23

Nunan N, Schmidt H, X Raynaud (2020)

The ecology of heterogeneity: soil bacterial communities and C dynamics.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1798):20190249.

Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

RevDate: 2020-03-22

Ferreira DA, da Silva TF, Pylro VS, et al (2020)

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.

Microbial ecology pii:10.1007/s00248-020-01502-z [Epub ahead of print].

Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.

RevDate: 2020-03-22

Santos A, Rachid C, Pacheco AB, et al (2020)

Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.

Microbiological research, 236:126452 pii:S0944-5013(19)30600-7 [Epub ahead of print].

Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.

RevDate: 2020-03-21

Chatzigiannidou I, Teughels W, Van de Wiele T, et al (2020)

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile.

NPJ biofilms and microbiomes, 6(1):13 pii:10.1038/s41522-020-0124-3.

Oral diseases (e.g., dental caries, periodontitis) are developed when the healthy oral microbiome is imbalanced allowing the increase of pathobiont strains. Common practice to prevent or treat such diseases is the use of antiseptics, like chlorhexidine. However, the impact of these antiseptics on the composition and metabolic activity of the oral microbiome is poorly addressed. Using two types of oral biofilms-a 14-species community (more controllable) and human tongue microbiota (more representative)-the impact of short-term chlorhexidine exposure was explored in-depth. In both models, oral biofilms treated with chlorhexidine exhibited a pattern of inactivation (>3 log units) and fast regrowth to the initial bacterial concentrations. Moreover, the chlorhexidine treatment induced profound shifts in microbiota composition and metabolic activity. In some cases, disease associated traits were increased (such as higher abundance of pathobiont strains or shift in high lactate production). Our results highlight the need for alternative treatments that selectively target the disease-associated bacteria in the biofilm without targeting the commensal microorganisms.

RevDate: 2020-03-20

Farhana L, Sarkar S, Nangia-Makker P, et al (2020)

Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.

PloS one, 15(3):e0229823 pii:PONE-D-19-08167.

The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.

RevDate: 2020-03-20

Ghosh A, Debnath M, P Bhadury (2020)

Datasets of surface water microbial populations from two anthropogenically impacted sites on the Bhagirathi-Hooghly River.

Data in brief, 29:105371 pii:105371.

The Bhagirathi-Hooghly River, part of the River Ganga, flows along densely urbanized areas in West Bengal, India. The River water is extensively used for household activities, human consumption including bathing, social purposes and multifaceted industrial usage. As a result of discharge of untreated municipal sewage and effluents from industries there is evidence of heavy pollution in this River. Two urbanized sites on the Bhagirathi-Hooghly River, namely Kalyani and Kolkata, were sampled to elucidate the resident microbial communities in lieu of anthropogenic forcing with respect to pollution. The Kalyani station (Kal_Stn1) lies upstream to the Kolkata station (Kol_Stn7) and are approximate 50 km away from each other and located along the bank of Bhagirathi-Hooghly River. Sampling was undertaken in monsoon (September 2018). In situ environmental parameters were measured during sampling and dissolved nutrients were estimated from formalin fixed filtered surface water along with pesticides analysis. One litre surface water sample was collected from each station and environmental DNA was sequenced to identify resident microbial communities (bacterioplankton and oxygenic photoautrophs-phytoplankton). The bacterioplankton community structure was elucidated by sequencing the V4 region of the 16S rDNA on an Illumina MiSeq platform. Proteobacteria was found to be the most abundant bacterioplankton phylum in both sampling stations. Similar to bacterioplankton, variation in oxygenic photoautotrophic community structure including phytoplankton forms was found at phylum, class and family levels. The phytoplankton communities were elucidated by sequencing the V9 region of the 18S rDNA on an Illumina MiSeq platform. Chrysophyta was found to be the most abundant phytoplankton phylum identified from both stations, followed by Chlorophyta and other groups. Variation in phytoplankton community structure between the stations was distinct at phylum, class and family levels.

RevDate: 2020-03-20

Gueneau R, Blanchet D, Rodriguez-Nava V, et al (2020)

Actinomycetoma caused by Gordonia westfalica: first reported case of human infection.

New microbes and new infections, 34:100658 pii:100658.

Bacteria of the genus Gordonia are rarely involved in human infections. We report here the case of a 30-year-old man from Guinea Buissau with mycetoma of the foot. 16S DNA sequencing after surgical biopsy identified Gordonia westfalica. To our knowledge, this is the first report of human infection caused by G. westfalica.

RevDate: 2020-03-20

Flores N, Hoyos S, Venegas M, et al (2020)

Haloterrigena sp. Strain SGH1, a Bacterioruberin-Rich, Perchlorate-Tolerant Halophilic Archaeon Isolated From Halite Microbial Communities, Atacama Desert, Chile.

Frontiers in microbiology, 11:324.

An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids. Growth was severely restricted at salinities below 15% NaCl and cell lysis is avoided at a minimal 10% NaCl. Maximal concentrations of magnesium chloride and sodium or magnesium perchlorates that supported SGH1 growth were 0.5 and 0.15M, respectively. Haloterrigena sp. strain SGH1 accumulates bacterioruberin (BR), a C50 xanthophyll, as the major carotenoid. Total carotenoids in strain SGH1 amounted to nearly 400 μg BR per gram of dry biomass. Nearly 80% of total carotenoids accumulated as geometric isomers of BR: all-trans-BR (50%), 5-cis-BR (15%), 9-cis-BR (10%), 13-cis-BR (4%); other carotenoids were dehydrated derivatives of BR. Carotenogenesis in SGH1 was a reversible and salt-dependent process; transferring BR-rich cells grown in 25% (w/v) NaCl to 15% (w/v) NaCl medium resulted in depigmentation, and BR content was recovered after transference and growth of unpigmented cells to high salinity medium. Methanol extracts and purified BR isomers showed an 8-9-fold higher antioxidant activity than Trolox or β-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells.

RevDate: 2020-03-20

Cortes-Tolalpa L, Wang Y, Salles JF, et al (2020)

Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15.

Frontiers in microbiology, 11:248.

Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.

RevDate: 2020-03-20

Corti-Monzón G, Nisenbaum M, Villegas-Plazas M, et al (2020)

Enrichment and characterization of a bilge microbial consortium with oil in water-emulsions breaking ability for oily wastewater treatment.

Biodegradation pii:10.1007/s10532-020-09894-y [Epub ahead of print].

Oily bilge wastewater is one of the main sources of hydrocarbons pollution in marine environments due to accidental or clandestine discharges. The main technical challenge for its effective treatment is the presence of stable oil-in-water (O/W) emulsions. In this work we are reporting an enriched microbial consortium from bilge wastewater with remarkable ability to demulsify oil in water emulsions. The consortium showed emulsion-breaking ratios up to 72.6% in the exponential growth phase, while the values range from 11.9 to 8.5% in stationary phase. A positive association was observed between demulsifying ability and microbial adhesion to hydrocarbons, as well as between cell concentration and demulsifying ability. Also, an interesting ability to demulsify under different temperatures, conditions of agitation, and bilge emulsions from different vessels was observed. The Bacterial and Archaeal composition was analyzed by 16S rRNA gene amplicon lllumina sequencing analyses, revealing an assemblage composed of bacterial types highly related to well characterized bacterial isolates and also to non-yet cultured bacterial types previously detected in marine and sediment samples. Hydrocarbonoclastic microbial types such as Marinobacter, Flavobacteriaceae, Alcanivorax and Gammaproteobacteria PYR10d3 were found in high relative abundance (27.0%-11.1%) and types of marine oligotrophs and surfactant degraders such as Thallasospira, Parvibaculum, Novospirillum, Shewanella algae, and Opitutae were in a group of middle predominance (1.7-3.5%). The microbial consortium reported has promising potential for the biological demulsification of bilge wastewater and other oily wastewaters.

RevDate: 2020-03-20

Kavagutti VS, Andrei AŞ, Mehrshad M, et al (2020)

Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.

Microbiome, 8(1):40 pii:10.1186/s40168-020-00828-7.

Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.

RevDate: 2020-03-19

Dini-Andreote F (2020)

Endophytes: The Second Layer of Plant Defense.

Trends in plant science, 25(4):319-322.

Microorganisms in association with roots can protect plants against soil-borne diseases. A recent study mechanistically revealed how root endophytes act as a second microbiological layer of plant defense. Integrating ecological concepts with principles of plant pathology provides an innovative way to manipulate and engineer beneficial plant microbiomes.

RevDate: 2020-03-19

Tinker KA, EA Ottesen (2020)

Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea).

Applied and environmental microbiology, 86(7): pii:AEM.02513-19.

The gut microbiome is shaped by both host diet and host phylogeny. However, separating the relative influence of these two factors over long periods of evolutionary time is often difficult. We conducted a 16S rRNA gene amplicon-based survey of the gut microbiome from 237 individuals and 19 species of omnivorous cockroaches from the order Blattodea. The order Blattodea represents an ancient lineage of insects that emerged over 300 million years ago, have a diverse gut microbiota, and have a typically gregarious lifestyle. All cockroaches shared a broadly similar gut microbiota, with 66 microbial families present across all species and 13 present in every individual examined. Although our network analysis of the cockroach gut microbiome showed a large amount of connectivity, we demonstrated that gut microbiota cluster strongly by host species. We conducted follow-up tests to determine if cockroaches exhibit phylosymbiosis, or the tendency of host-associated microbial communities to parallel the phylogeny of related host species. Across the full data set, gut microbial community similarity was not found to correlate with host phylogenetic distance. However, a weak but significant phylosymbiotic signature was observed using the matching cluster metric, which allows for localized changes within a phylogenetic tree that are more likely to occur over long evolutionary distances. This finding suggests that host phylogeny plays a large role in structuring the cockroach gut microbiome over shorter evolutionary distances and a weak but significant role in shaping the gut microbiome over extended periods of evolutionary time.IMPORTANCE The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a strong relationship between host species identity and gut microbiome composition and found a weaker but significant role for host phylogeny in determining microbiome similarity over extended periods of evolutionary time. This study advances our understanding of the role of host phylogeny in shaping the gut microbiome over different evolutionary distances.

RevDate: 2020-03-18

Pu X, Li Z, Tian Y, et al (2020)

The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration.

The New phytologist [Epub ahead of print].

Lonicera japonica is a wide-spread member of the Caprifoliaceae (honeysuckle) family utilized in traditional medical practices. This twining vine honeysuckle is also a much-sought ornamental, in part due to its dynamic flower coloration, which changes from white to gold during development. The molecular mechanism underlying dynamic flower coloration in L. japonica was elucidated by integrating whole genome sequencing, transcriptomic analysis, and biochemical assays. Here, we report a chromosome-level genome assembly of L. japonica, comprising nine pseudo-chromosomes with a total size of 843.2 Mb. We also provide evidence for a whole genome duplication event in the lineage leading to L. japonica, which occurred after its divergence from Dipsacales and Asterales. Moreover, gene expression analysis not only revealed correlated expression of the relevant biosynthetic genes with carotenoid accumulation, but also suggested a role for carotenoid degradation in L. japonica's dynamic flower coloration. The variation of flower color is consistent with not only the observed carotenoid accumulation pattern, but also with the release of volatile apocarotenoids that presumably serve as pollinator attractants. Beyond novel insights into the evolution and dynamics of flower coloration, the high-quality L. japonica genome sequence also provides a foundation for molecular breeding to improve desired characteristics.

RevDate: 2020-03-18

Danczak RE, Daly RA, Borton MA, et al (2020)

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems.

mSystems, 5(2): pii:5/2/e00098-20.

The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.

RevDate: 2020-03-18

Fu S, Wei D, Yang Q, et al (2020)

Horizontal Plasmid Transfer Promotes the Dissemination of Asian Acute Hepatopancreatic Necrosis Disease and Provides a Novel Mechanism for Genetic Exchange and Environmental Adaptation.

mSystems, 5(2): pii:5/2/e00799-19.

Vibrio parahaemolyticus is an important foodborne pathogen and has recently gained particular notoriety because it causes acute hepatopancreatic necrosis disease (AHPND) in shrimp, which has caused significant economic loss in the shrimp industry. Here, we report a whole-genome analysis of 233 V. parahaemolyticus strains isolated from humans, diseased shrimp, and environmental samples collected between 2008 and 2017, providing unprecedented insight into the historical spread of AHPND. The results show that V. parahaemolyticus is genetically diverse and can be divided into 84 sequence types (STs). However, genomic analysis of three STs of V. parahaemolyticus identified seven transmission routes in Asia since 1996, which promoted the transfer of an AHPND-associated plasmid. Notably, the insertion sequence (ISVal1) from the plasmid subsequently mediated the genetic exchange among V. parahaemolyticus STs and resulted in the deletion of an 11-kb region regulating cell mobility and the production of capsular polysaccharides. Phenotype assays confirmed that this deletion enhanced biofilm formation, providing a novel mechanism for environmental adaptation. We conclude that the transmission mode of AHPND consists of two steps, the transmission of V. parahaemolyticus and the subsequent horizontal transfer of the AHPND-associated plasmid. This plasmid allows ISVal1 to mediate genetic exchange and improve pathogen fitness in shrimp ponds. Current shrimp farming practices promoted such genetic exchanges, which highlighted a risk of the emergence of new virulent populations, with potentially devastating consequences for both aquaculture and human health. This study addressed the basic questions regarding the transmission mechanism of AHPND and provided novel insights into shrimp and human disease management.IMPORTANCE Global outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the horizontal transfer of an AHPND-associated plasmid. Surprisingly, the introduction of the AHPND-associated plasmid also offers a novel mechanism of genetic exchange mediated by insertion sequences, and it improved the fitness of V. parahaemolyticus in a harsh environment. The results presented herein suggest that current shrimp farming practices promote genetic mixture between endemic and oceanic V. parahaemolyticus populations, which introduced the plasmid and accelerated bacterial adaptation by the acquisition of ecologically important functions. This entails a risk of the emergence of new virulent populations both for shrimp and humans. This study improves our understanding of the global dissemination of the AHPND-associated plasmid and highlights the urgent need to improve biosecurity for shrimp farming.

RevDate: 2020-03-18

Yang Y, Daims H, Liu Y, et al (2020)

Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

mBio, 11(2): pii:mBio.03175-19.

The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.

RevDate: 2020-03-17

Spanoghe J, Grunert O, Wambacq E, et al (2020)

Storage, fertilization and cost properties highlight the potential of dried microbial biomass as organic fertilizer.

Microbial biotechnology [Epub ahead of print].

The transition to sustainable agriculture and horticulture is a societal challenge of global importance. Fertilization with a minimum impact on the environment can facilitate this. Organic fertilizers can play an important role, given their typical release pattern and production through resource recovery. Microbial fertilizers (MFs) constitute an emerging class of organic fertilizers and consist of dried microbial biomass, for instance produced on effluents from the food and beverage industry. In this study, three groups of organisms were tested as MFs: a high-rate consortium aerobic bacteria (CAB), the microalga Arthrospira platensis ('Spirulina') and a purple non-sulfur bacterium (PNSB) Rhodobacter sp. During storage as dry products, the MFs showed light hygroscopic activity, but the mineral and organic fractions remained stable over a storage period of 91 days. For biological tests, a reference organic fertilizer (ROF) was used as positive control, and a commercial organic growing medium (GM) as substrate. The mineralization patterns without and with plants were similar for all MFs and ROF, with more than 70% of the organic nitrogen mineralized in 77 days. In a first fertilization trial with parsley, all MFs showed equal performance compared to ROF, and the plant fresh weight was even higher with CAB fertilization. CAB was subsequently used in a follow-up trial with petunia and resulted in elevated plant height, comparable chlorophyll content and a higher amount of flowers compared to ROF. Finally, a cost estimation for packed GM with supplemented fertilizer indicated that CAB and a blend of CAB/PNSB (85%/15%) were most cost competitive, with an increase of 6% and 7% in cost compared to ROF. In conclusion, as bio-based fertilizers, MFs have the potential to contribute to sustainable plant nutrition, performing as good as a commercially available organic fertilizer, and to a circular economy.

RevDate: 2020-03-17

Byers AK, Condron L, Donavan T, et al (2020)

Soil microbial diversity in adjacent forest systems- contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest.

FEMS microbiology ecology pii:5808812 [Epub ahead of print].

Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with less than 1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) is significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using NGS-based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.

RevDate: 2020-03-17

Gurmessa B, Pedretti EF, Cocco S, et al (2020)

Manure anaerobic digestion effects and the role of pre- and post-treatments on veterinary antibiotics and antibiotic resistance genes removal efficiency.

The Science of the total environment, 721:137532 pii:S0048-9697(20)31043-3 [Epub ahead of print].

This review was aimed to summarize and critically evaluate studies on removal of veterinary antibiotics (VAs), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) with anaerobic digestion (AD) of manure and demonstrate areas of focus for improved removal efficiency. The environmental risks associated to the release of the same were also critically evaluated. The potential of AD and advanced AD of manure on removal rate of VAs, ARGs and MGEs was thoroughly assessed. In addition, the role of post and pre-AD treatments and their potential to support VAs and ARGs removal efficiency were evaluated. The overall review results show disparity among the different groups of VAs in terms of removal rate with relatively higher efficiency for β-lactams and tetracyclines compared to the other groups. Some of sulfonamides, fluoroquinolones and macrolides were reported to be highly persistent with removal rates as low as zero. Within group differences were also reported in many literatures. Moreover, removal of ARGs and MGEs by AD was widely reported although complete removal was hardly possible. Even in rare scenarios, some AD conditions were reported to increase copies of specific groups of the genes. Temperature pretreatments and temperature phased advanced AD were also reported to improve removal efficiency of VAs while contributing to increased biogas production. Moreover, a few studies also showed the possibility of further removal by post-AD treatments such as liquid-solid separation, drying and composting. In conclusion, the various studies revealed that AD in its current technological level is not a guarantee for complete removal of VAs, ARGs and MGEs from manure. Consequently, their possible release to the soils with digestate could threaten the healthcare and disturb soil microbial ecology. Thus, intensive management strategies need to be designed to increase removal efficiency at the different manure management points along the anaerobic digestion process.

RevDate: 2020-03-16

Ruiz C, Villegas-Plazas M, Thomas OP, et al (2020)

Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha).

FEMS microbiology ecology pii:5807073 [Epub ahead of print].

The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha, and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: 1 Homoscleromopha of the Oscarellidae family and 4 Demospongiae. A total of 256,458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by 5 OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

RevDate: 2020-03-15

Wen D, Valencia A, Ordonez D, et al (2020)

Comparative nitrogen removal via microbial ecology between soil and green sorption media in a rapid infiltration basin for co-disposal of stormwater and wastewater.

Environmental research, 184:109338 pii:S0013-9351(20)30231-0 [Epub ahead of print].

In this study, a rapid infiltration basin (RIB) designed as green infrastructure for co-disposal of wastewater effluent and stormwater runoff was retrofitted for sustainable groundwater recharge after nitrogen removal. For comparison of nitrogen removal efficiency via different filtration media, the RIB was divided into two sub-basins for different filtration processes. One sub-basin was filled with a native sandy soil with about 2-4% clay (Control RIB), and the other sub-basin was modified with Biosorption Activated Media (BAM) (BAM RIB), for the enhancement of microbial nitrogen removal. The two sub-basins accept an equal amount of excess reclaimed wastewater in non-storm periods, and stormwater during periodic storm events. The infiltrate in both the BAM RIB and the Control RIB eventually reaches the Upper Floridan Aquifer. The seven microbial species involved in this microbial ecology study are nitrite oxidizing bacteria (NOB), ammonia oxidizing bacteria (AOB), anaerobic oxidation of ammonium (anammox) bacteria, complete ammonia oxidizer (Comammox) bacteria, denitrifiers, dissimilatory nitrate reduction to ammonium (DNRA) and ammonia-oxidizing archaea (AOA). The population dynamics study was conducted with the aid of the quantitative polymerase chain reaction (qPCR) for the quantification of the microbial gene population in support of microbial ecology discovery. The qPCR results demonstrated the competition effect between AOA, AOB, and Comammox, the inhibition effect between NOB and DNRA with the presence of anammox, and the complementary effect due to an abundance of NOB and AOB in the microbial ecology. Although, competition between denitrifiers and DNRA was expected to impact population dynamics, both microbial species were found to be the most predominant in both control and BAM RIBs. Research findings indicate that the use of BAM RIB achieves significantly efficient nitrogen removal driven by complementary effects in the microbial ecology.

RevDate: 2020-03-15

Garin-Fernandez A, Glöckner FO, A Wichels (2020)

Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus.

Marine genomics pii:S1874-7787(20)30028-3 [Epub ahead of print].

The seawater temperature rise can promote the growth of potentially pathogenic Vibrio species. In the North Sea, V. parahaemolyticus strains have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment. Here, we present the genome structure and possible biological functions of the inducible phage vB_VpaI_VP-3218, a novel filamentous phage carried by the V. parahaemolyticus strain VN-3218. Prophages of the strain VN-3218 were induced with mitomycin C and the DNA from the phage induction was sequenced. Two incomplete prophages were identified, only one complete phage genome with length of 11,082 bp was characterized. The phage vB_VpaI_VP-3218 belongs to the Inoviridae family and shows close homology to the Saetivirus genus. This phage can integrate into the chromosomal host genome and carries host-related regions absent in similar phage genomes, suggesting that this phage might integrate in other Vibrio host genomes from the environment. Furthermore, this phage might have a role in pathogenicity due to potential zonula occludens toxin genes. Based on its genomic similarity, the genome of vB_VpaI_VP-3218 phage probably integrates into the lysogen's chromosome and replicates as episome. This study complements prophage induction and bioinformatic studies applied to non-model species of potentially pathogenic Vibrio species. The characterization of this phage provides new insights with respect to the presence of filamentous phages in environmental V. parahaemolyticus strains, which might have a role in the emergence of new pathogenic strains in the North Sea.

RevDate: 2020-03-14

Props R, VJ Denef (2020)

Temperature and nutrient levels correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus.

Applied and environmental microbiology pii:AEM.00140-20 [Epub ahead of print].

Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. Additionally, strains predominant in low and high phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification, and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.ImportanceLimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple co-occurring populations of which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.

RevDate: 2020-03-13

Paramasivan S, Bassiouni A, Shiffer A, et al (2020)

The international sinonasal microbiome study (ISMS): a multi-centre, multi-national characterization of sinonasal bacterial ecology.

Allergy [Epub ahead of print].

The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterise the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus, and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. Amongst patients suffering from CRS with nasal polyps, a statistically significant reduction in relative abundance of Corynebacterium (40.29% vs 50.43%; p = 0.02) was identified. Despite some measured differences in microbiome composition and diversity between some of the participating centres in our cohort, these differences would not alter the general pattern of core organisms described. Nevertheless, atypical or unusual organisms reported in short-read amplicon sequencing studies and that are not part of the core microbiome should be interpreted with caution. The delineation of the sinonasal microbiome and standardised methodology described within our study will enable further characterisation and translational application of the sinus microbiota.

RevDate: 2020-03-12

van Hougenhouck-Tulleken WG, Lebre PH, Said M, et al (2020)

Bacterial pathogens in peritoneal dialysis peritonitis: Insights from next-generation sequencing.

Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis [Epub ahead of print].

BACKGROUND: Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms.

METHODS: In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-generation sequencing (NGS) techniques.

RESULTS: Total concordance between culture and NGS was noted. In addition, the NGS technique was highly sensitive, identifying 33 different bacteria (including a nonculturable bacterium), compared to 13 bacterial species using culture-based techniques. This was counterbalanced by a lack of specificity with NGS, largely due to the small size of the 16S rRNA gene segment sequenced.

CONCLUSIONS: For the clinician, our results suggest that PD peritonitis may often be a polymicrobial disease and that treating a dominant organism may not totally eradicate all bacterial contamination within the peritoneum. For the clinical scientist, additional use of a larger 16S rRNA segment (V5 or V6) is likely to outperform the use of the V4 segment only.

RevDate: 2020-03-12

Neissi A, Rafiee G, Farahmand H, et al (2020)

Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss).

Microbial ecology pii:10.1007/s00248-020-01498-6 [Epub ahead of print].

The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.

RevDate: 2020-03-11

Glodowska M, Stopelli E, Schneider M, et al (2020)

Role of in Situ Natural Organic Matter in Mobilizing As during Microbial Reduction of FeIII-Mineral-Bearing Aquifer Sediments from Hanoi (Vietnam).

Environmental science & technology [Epub ahead of print].

Natural organic matter (NOM) can contribute to arsenic (As) mobilization as an electron donor for microbially-mediated reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides. However, to investigate this process, instead of using NOM, most laboratory studies used simple fatty acids or sugars, often at relatively high concentrations. To investigate the role of relevant C sources, we therefore extracted in situ NOM from the upper aquitard (clayey silt) and lower sandy aquifer sediments in Van Phuc (Hanoi area, Vietnam), characterized its composition, and used 100-day microcosm experiments to determine the effect of in situ OM on Fe(III) mineral reduction, As mobilization, and microbial community composition. We found that OM extracted from the clayey silt (OMC) aquitard resembles young, not fully degraded plant-related material, while OM from the sandy sediments (OMS) is more bioavailable and related to microbial biomass. Although all microcosms were amended with the same amount of C (12 mg C/L), the extent of Fe(III) reduction after 100 days was the highest with acetate/lactate (43 ± 3.5% of total Fe present in the sediments) followed by OMS (28 ± 0.3%) and OMC (19 ± 0.8%). Initial Fe(III) reduction rates were also higher with acetate/lactate (0.53 mg Fe(II) in 6 days) than with OMS and OMC (0.18 and 0.08 mg Fe(II) in 6 days, respectively). Although initially more dissolved As was detected in the acetate/lactate setups, after 100 days, higher concentrations of As (8.3 ± 0.3 and 8.8 ± 0.8 μg As/L) were reached in OMC and OMS, respectively, compared to acetate/lactate-amended setups (6.3 ± 0.7 μg As/L). 16S rRNA amplicon sequence analyses revealed that acetate/lactate mainly enriched Geobacter, while in situ OM supported growth and activity of a more diverse microbial community. Our results suggest that although the in situ NOM is less efficient in stimulating microbial Fe(III) reduction than highly bioavailable acetate/lactate, it ultimately has the potential to mobilize the same amount or even more As.

RevDate: 2020-03-11

Stastney P, S Black (2020)

Bog Microtopography and the Climatic Sensitivity of Testate Amoeba Communities: Implications for Transfer Function-Based Paleo-Water Table Reconstructions.

Microbial ecology pii:10.1007/s00248-020-01499-5 [Epub ahead of print].

Although the use of sub-fossil testate amoebae as a proxy for raised bog hydrology in Holocene paleoecological studies is well-established, some detailed aspects of species-environment relationships remain under-researched. One such issue is the effect of bog surface microtopography on the climatic sensitivity of testate amoeba communities. Although it has been suggested that some microforms-especially hummocks-may be less sensitive to climatic forcing than others, this has rarely been objectively tested. To investigate this, subfossil testate amoebae assemblages have been examined in a series of shallow cores collected along a hummock-lawn-hollow transect from a bog in central Ireland and the resulting reconstructed water table records, dated using 210Pb, have been compared with instrumental weather data. Testate amoebae communities in the hollow microform were found to be significantly less diverse than those in the hummock and lawn, and both the hummock and lawn showed statistically significant correlations with instrumental temperature and precipitation data. Therefore, whilst the suggestion that paleoecological investigations should target intermediate bog microforms remains sound, the notion that hummock-based testate amoebae hydrological data are climatically-insensitive is challenged.

RevDate: 2020-03-15

Alteio LV, Schulz F, Seshadri R, et al (2020)

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

mSystems, 5(2):.

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

RevDate: 2020-03-11

Cabello-Olmo M, Oneca M, Torre P, et al (2020)

Influence of Storage Temperature and Packaging on Bacteria and Yeast Viability in a Plant-Based Fermented Food.

Foods (Basel, Switzerland), 9(3): pii:foods9030302.

Optimization of food storage has become a central issue for food science and biotechnology, especially in the field of functional foods. The aim of this work was to investigate the influence of different storage strategies in a fermented food product (FFP) and further determine whether the regular storage (room temperature (RT) and standard packaging (SP)) could be refined. Eight experimental conditions (four different temperatures × two packaging) were simulated and changes in FFP's microbial ecology (total bacteria, lactic acid bacteria (LAB), and yeasts) and physicochemical characteristics (pH and moisture content (MC)) were determined following 1, 3, 6, and 12 months. All conditions tested showed a decline in microbial content due to the effect of the temperature, 37 °C being the most detrimental condition, while -20 and 4 °C seemed to be better than RT in some parameters. Vacuum packaging (VP) only had a major effect on MC and we found that VP preserved greater MC values than SP at 3, 6, and 12 months. The correlation analysis revealed that total bacteria, LAB, and yeasts were positively associated, and also both pH and MC showed a correlation. According to our results and with the purpose to maintain the load of viable microorganisms, we observed that the best storage conditions should contemplate SP and freezing or cooling temperature during a period no longer than 3 months.

RevDate: 2020-03-10

Moscoviz R, Quéméner ED, Trably E, et al (2020)

Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer.

Trends in microbiology, 28(4):245-253.

Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote competitive and even parasitic behaviour. Based on three interesting case studies identified from the literature, we also highlight that such nonmutualistic interactions could be widespread and of particular significance for the survival of pathogens or the shaping of complex microbial communities.

RevDate: 2020-03-10

Mukherjee S, Naha S, Bhadury P, et al (2020)

Emergence of OXA-232-producing hypervirulent Klebsiella pneumoniae ST23 causing neonatal sepsis.

The Journal of antimicrobial chemotherapy pii:5802604 [Epub ahead of print].

RevDate: 2020-03-13

Cliffe L, Nixon SL, Daly RA, et al (2020)

Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters.

Frontiers in microbiology, 11:286.

Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of "sour gas" which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.

RevDate: 2020-03-10

Chriswell ME, KA Kuhn (2020)

Microbiota-mediated mucosal inflammation in arthritis.

Best practice & research. Clinical rheumatology pii:S1521-6942(20)30009-7 [Epub ahead of print].

Mucosal surfaces are a unique symbiotic environment between a host and a vast and diverse ecology of microbes. These microbes have great immunomodulatory potential with respect to the host organism. Indeed, the mucosal immune system strikes a delicate balance between tolerance of commensal organisms and overt inflammation to ward off pathogens. Disruptions of the microbial ecology at mucosal surfaces has been described in a vast number of different human disease processes including many forms of arthritis, and the resulting implications are still being understood to their fullest. Herein, we review the current state of knowledge in microbe-host interactions as it relates to the development of arthritis through bacterial translocation, bacterial metabolite production, education of the immune response, and molecular mimicry.

RevDate: 2020-03-13

Moore RM, Harrison AO, McAllister SM, et al (2020)

Iroki: automatic customization and visualization of phylogenetic trees.

PeerJ, 8:e8584.

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

RevDate: 2020-03-07

Nuzzo A, Satpute A, Albrecht U, et al (2020)

Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil.

Microbial ecology pii:10.1007/s00248-020-01497-7 [Epub ahead of print].

There is increased interest by the agricultural industry in microbial amendments that leverage natural beneficial interactions between plants and soil microbes to improve crop production. However, translating fundamental knowledge from laboratory experiments into efficient field application often has mixed results, and there is less clarity about the interaction between added microbes and the native microbial community, where microorganisms belonging to the same phylogenic clades often reside. In this study, four commercially available microbial amendments were examined in two greenhouse experiments using field soil to assess their impact on tomato plant growth and the native soil microbial communities. The amendments contained different formulations of plant growth-promoting bacteria (Lactobacilli, Rhizobia, etc.), yeasts, and mycorrhizal fungi. The application of the tested amendments in greenhouse conditions resulted in no significant impact on plant growth. A deeper statistical analysis detected variations in the microbial communities that accounted only for 0.25% of the total species, particularly in native taxa not related to the inoculated species and represented less than 1% of the total variance. This suggests that under commercial field conditions, additional confounding variables may play a role in the efficacy of soil microbial amendments. This study confirms the necessity of more in-depth validation requirements for the formulations of soil microbial amendments before delivery to the agricultural market in order to leverage their benefits for the producers, the consumers, and the environment.

RevDate: 2020-03-07

Zhang Y, Hao X, Garcia-Lemos AM, et al (2020)

Soil fertilization has different effects on bacterial community composition in the Penicillium canescens hyphosphere and in bulk soil.

Applied and environmental microbiology pii:AEM.02969-19 [Epub ahead of print].

This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. Compared with the soil communities, P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria. As core bacterial taxa, Delftia and Pseudomonas were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition and distinctive taxa/OTUs of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate a P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes compared to soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities indicating an, at least partly, anoxic microenvironment with high carbon to N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.IMPORTANCE P-solubilizing Penicillium spp. strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Beta- and Gammaproteobacteria colonize P. canescens hyphae in soil, and that the composition of these communities depends on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P and points to the hyphosphere as a hotspot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for future optimization of next-generation biofertilizer consortia for applications in soil.

RevDate: 2020-03-10

Song J, Jongmans-Hochschulz E, Mauder N, et al (2020)

The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany).

The Science of the total environment, 720:137603 pii:S0048-9697(20)31114-1 [Epub ahead of print].

The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.

RevDate: 2020-03-08

Pascoal F, Magalhães C, R Costa (2020)

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential.

Frontiers in microbiology, 11:231.

Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.

RevDate: 2020-03-06

Charmpi C, Van der Veken D, Van Reckem E, et al (2020)

Raw meat quality and salt levels affect the bacterial species diversity and community dynamics during the fermentation of pork mince.

Food microbiology, 89:103434.

Acidification level and temperature modulate the beneficial consortia of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS) during meat fermentation. Less is known about the impact of other factors, such as raw meat quality and salting. These could for instance affect the growth of the pathogen Staphylococcus aureus or of Enterobacterales species, potentially indicative of poor fermentation practice. Therefore, pork batters from either normal or borderline quality (dark-firm-dry, DFD) were compared at various salt concentrations (0-4%) in meat fermentation models. Microbial ecology of the samples was investigated with culture-dependent techniques and (GTG)5-PCR fingerprinting of genomic DNA. Whilst Lactobacillus sakei governed the fermentation of normal meat, Lactobacillus curvatus was more prominent in the fermentation of the DFD meat variant. CNS were favoured during fermentation at rising salt concentrations without much effects on species diversity, consisting mostly of Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. During fermentation of DFD meat, S. saprophyticus was less manifest than during that of normal meat. Enterobacterales mainly emerged in DFD meat during fermentation at low salt concentrations. The salt hurdle was insufficient to prevent Enterobacterales when acidification and initial pH were favourable for their growth.

RevDate: 2020-03-06

Tian Y, Gui W, Koo I, et al (2020)

The microbiome modulating activity of bile acids.

Gut microbes [Epub ahead of print].

Bile acids are potent antibacterial compounds and play an important role in shaping the microbial ecology of the gut. Here, we combined flow cytometry, growth rate measurements (OD600), and NMR- and mass spectrometry-based metabolomics to systematically profile the impact of bile acids on the microbiome using in vitro and in vivo models. This study confirmed that (1) unconjugated bile acids possess more potent antibacterial activity than conjugated bile acids; (2) Gram-positive bacteria are more sensitive to bile acids than Gram-negative bacteria; (3) some probiotic bacteria such as Lactobacillus and Bifidobacterium and 7α-dehydroxylating bacteria such as Clostridium scindens show bile acid resistance that is associated with activation of glycolysis. Moreover, we demonstrated that (4) as one of most hydrophobic bile acids, lithocholic acid (LCA) shows reduced toxicity to bacteria in the cecal microbiome in both in vivo and in vitro models; (5) bile acids directly and rapidly affect bacterial global metabolism including membrane damage, disrupted amino acid, nucleotide, and carbohydrate metabolism; and (6) in vivo, short-term exposure to bile acids significantly affected host metabolism via alterations of the bacterial community structure. This study systematically profiled interactions between bile acids and gut bacteria providing validation of previous observation and new insights into the interaction of bile acids with the microbiome and mechanisms related to bile acid tolerance.

RevDate: 2020-03-06

Gutiérrez-Sarmiento W, Sáyago-Ayerdi SG, Goñi I, et al (2020)

Changes in Intestinal Microbiota and Predicted Metabolic Pathways During Colonic Fermentation of Mango (Mangifera indica L.)-Based Bar Indigestible Fraction.

Nutrients, 12(3): pii:nu12030683.

Mango (Mangifera indica L.) peel and pulp are a source of dietary fiber (DF) and phenolic compounds (PCs) that constituent part of the indigestible fraction (IF). This fraction reaches the colon and acts as a carbon and energy source for intestinal microbiota. The effect of mango IF on intestinal microbiota during colonic fermentation is unknown. In this study, the isolated IF of a novel 'Ataulfo' mango-based bar (snack) UV-C irradiated and non-irradiated (UVMangoB and MangoB) were fermented. Colonic fermentation occurred in vitro under chemical-enzymatic, semi-anaerobic, batch culture and controlled pH colonic conditions. Changes in the structure of fecal microbiota were analyzed by 16s rRNA gene Illumina MiSeq sequencing. The community´s functional capabilities were determined in silico. The MangoB and UVMangoB increased the presence of Faecalibacterium, Roseburia, Eubacterium, Fusicatenibacter, Holdemanella, Catenibacterium, Phascolarctobacterium, Buttiauxella, Bifidobacterium,Collinsella, Prevotella and Bacteroides genera. The alpha indexes showed a decrease in microbial diversity after 6 h of colonic fermentation. The coordinates analysis indicated any differences between irradiated and non-irradiated bar. The metabolic prediction demonstrated that MangoB and UVMangoB increase the microbiota carbohydrate metabolism pathway. This study suggests that IF of mango-based bar induced beneficial changes on microbial ecology and metabolic pathway that could be promissory to prevention or treatment of metabolic dysbiosis. However, in vivo interventions are necessary to confirm the interactions between microbiota modulating and intestinal beneficial effects.

RevDate: 2020-03-05

Weis S, Schnell S, M Egert (2020)

Towards Safer-SIP - Effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation.

Canadian journal of microbiology [Epub ahead of print].

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community to the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopically labeled from unlabeled RNA by isopycnic density ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a similar distribution pattern as if formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled from unlabeled RNA, which, however, has to be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.

RevDate: 2020-03-10
CmpDate: 2020-03-10

Gignoux-Wolfsohn SA, Precht WF, Peters EC, et al (2020)

Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis.

Diseases of aquatic organisms, 137(3):217-237.

This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.

RevDate: 2020-03-13

Mastrorilli E, Petrin S, Orsini M, et al (2020)

Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017.

BMC genomics, 21(1):202.

BACKGROUND: Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars.

RESULTS: 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans.

CONCLUSIONS: Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.

RevDate: 2020-03-12

Tu Q (2020)

Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity.

Environmental microbiology [Epub ahead of print].

Revealing the spatial scaling patterns of microbial diversity is of special interest in microbial ecology. One critical question is whether the observed spatial turnover rate truly reflect the actual spatial patterns of extremely diverse microbial communities. Using simulated mock communities, this study suggested that the currently observed microbial spatial turnover rates were overestimated by random sampling processes associated with high-throughput metagenomic sequencing. The observed z values were largely contributed by accumulated microbial taxa due to cumulative number of samples. This is a crucial issue because microbial communities already have very low spatial turnover rate due to the small size and potential cosmopolitism nature of microorganisms. Further investigations suggested a linear relationship between the observed and expected z values, which can be applied to remove random sampling noises from the observed z values. Adjustment of z values for data sets from six American forests showed much lower spatial turnover rate than that before adjustment. However, the patterns of z values among these six forests remained unchanged. This study suggested that our current understanding of microbial taxa-area relationships could be inaccurate. Therefore, cautions and efforts should be made for more accurate estimation and interpretation of microbial spatial patterns.

RevDate: 2020-03-03

Ntagia E, Chatzigiannidou I, Williamson AJ, et al (2020)

Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration.

Microbial biotechnology [Epub ahead of print].

Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h-1 were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50qAc) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.

RevDate: 2020-03-17

Hu X, Kerckhof FM, Ghesquière J, et al (2020)

Microbial Protein out of Thin Air: Fixation of Nitrogen Gas by an Autotrophic Hydrogen-Oxidizing Bacterial Enrichment.

Environmental science & technology, 54(6):3609-3617.

For the production of edible microbial protein (MP), ammonia generated by the Haber-Bosch process or reclaimed ammonia from waste streams is typically considered as the nitrogen source. These processes for ammonia production are highly energy intensive. In this study, the potential for using nitrogen gas (N2) as a direct nitrogen source for MP production by hydrogen-oxidizing bacteria (HOB) was evaluated. The use of N2 versus ammonium as nitrogen source during the enrichment process resulted in differentiation of the bacterial community composition of the enrichments. A few previously unknown potential N2-fixing HOB taxa (i.e., representatives of the genus Azonexus and the family Comamonadaceae) dominated the enrichments. The biomass yield of a N2-fixing HOB enrichment was 30-50% lower than that of the ammonium-based HOB enrichment from the same inoculum source. The dried biomass of N2-fixing HOB had a high protein content (62.0 ± 6.3%) and an essential amino acid profile comparable to MP from ammonium-based HOB. MP from N2-fixing HOB could potentially be produced in situ without entailing the emissions caused by ammonia production and transportation by conventional means. It could be a promising substitute for N2-fixing protein-rich soybean because it has 70% higher protein content and double energy conversion efficiency from solar energy to biomass.

RevDate: 2020-03-03

Rossmann M, Pérez-Jaramillo JE, Kavamura VN, et al (2020)

Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists.

FEMS microbiology ecology pii:5775476 [Epub ahead of print].

Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.

RevDate: 2020-03-03

O'Brien AM, Laurich J, Lash E, et al (2020)

Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor.

Microbial ecology pii:10.1007/s00248-019-01452-1 [Epub ahead of print].

The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.

RevDate: 2020-03-08

Romero Victorica M, Soria MA, Batista-García RA, et al (2020)

Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes.

Scientific reports, 10(1):3864.

In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.

RevDate: 2020-03-17

Ogbughalu OT, Vasileiadis S, Schumann RC, et al (2020)

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention.

Journal of hazardous materials, 393:122338 pii:S0304-3894(20)30326-5 [Epub ahead of print].

Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.

RevDate: 2020-03-05

Sarrocco S, Herrera-Estrella A, DB Collinge (2020)

Editorial: Plant Disease Management in the Post-genomic Era: From Functional Genomics to Genome Editing.

Frontiers in microbiology, 11:107.

RevDate: 2020-03-17

Cermak N, Datta MS, A Conwill (2020)

Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures.

iScience, 23(3):100915 pii:S2589-0042(20)30099-7 [Epub ahead of print].

Synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. Although next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we quantify amplicon composition in synthetic bacterial communities through Sanger sequencing. We PCR amplify a universal marker gene, then we sequence this amplicon mixture in a single Sanger sequencing reaction. We then fit the "mixed" electropherogram with contributions from each community member as a linear combination of time-warped single-strain electropherograms, allowing us to estimate the fractional amplicon abundance of each strain within the community. This approach can provide results within one day and costs ∼$5 per sample.

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In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )