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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 05 Jul 2020 at 01:34 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: 2020-07-03

Pinto OHB, Costa FS, Rodrigues GR, et al (2020)

Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids.

Microbial ecology pii:10.1007/s00248-020-01548-z [Epub ahead of print].

Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.

RevDate: 2020-07-02

Yang L, Hou K, Zhang B, et al (2020)

Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.

The Science of the total environment, 741:140423 pii:S0048-9697(20)33945-0 [Epub ahead of print].

With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.

RevDate: 2020-07-02

Kassaian N, Feizi A, Rostami S, et al (2020)

The effects of 6 mo of supplementation with probiotics and synbiotics on gut microbiota in the adults with prediabetes: A double blind randomized clinical trial.

Nutrition (Burbank, Los Angeles County, Calif.), 79-80:110854 pii:S0899-9007(20)30137-4 [Epub ahead of print].

OBJECTIVES: The evidence of 16S rRNA genes in the gut microbiota distinguished a higher Firmicutes-to-Bacteroidetes ratio in individuals who were obese and had diabetes than in a healthy cohort. So, it seems that the modulation of intestinal microbial ecology by pro-/pre-/synbiotics may contribute to the progression and prevention of metabolic diseases. The aim of this study was to assess the effects of probiotics and synbiotic supplementation on the modification of the intestinal microbiome in adults with prediabetes.

METHODS: In a randomized, double-blinded, placebo-controlled clinical trial, 120 patients with prediabetes were randomly assigned to consume 6 g/d of either a placebo containing maltodextrin (control) or multispecies probiotic or inulin-based synbiotic for 6 mo. Fecal samples were obtained at baseline and after 6 mo of supplementation. Dietary intake was assessed throughout the study (at baseline and after 3 and 6 mo). Total energy, macronutrients, and dietary fiber were calculated using a dietary program Nutritionist 4. DNA was extracted from fecal samples and the numbers of Clostridium perfringens (the represent of phylum Firmicutes), Bacteroides fragilis (the representative of Bacteroidetes) and Escherichia coli (as universal bacteria) were determined by quantitative real-time polymerase chain reactions (qPCR). The changes in the relative abundance of the two fecal bacteria before and after supplementation were analyzed and compared within and between groups.

RESULTS: There were no significant changes in dietary intake during the study. Six mo of supplementation with probiotics resulted in a statistically significant increase in the abundance of the B. fragilis-to-E.coli ratio (mean difference [MD] ± SE 0.47 ± 0.37, P = 0.04) and decrease of the relative proportion of Firmicutes-to-Bacteroidetes representatives (MD ± SE -118.8 ± 114.6, P = 0.02). Synbiotic had no significant effect on the changes in the bacteria. There were no significant differences between the three groups.

CONCLUSION: The results of this study suggest that manipulation of the human gut microbiome by using probiotics could provide a potential therapeutic approach in the prevention and management of obesity and metabolic disorders such as diabetes.

RevDate: 2020-07-02

Cheng XS, Huo YN, Fan YY, et al (2020)

Mindin serves as a tumour suppressor gene during colon cancer progression through MAPK/ERK signalling pathway in mice.

Journal of cellular and molecular medicine [Epub ahead of print].

Mindin is important in broad spectrum of immune responses. On the other hand, we previously reported that mindin attenuated human colon cancer development by blocking angiogenesis through Egr-1-mediated regulation. However, the mice original mindin directly suppressed the syngenic colorectal cancer (CRC) growth in our recent study and we aimed to further define the role of mindin during CRC development in mice. We established the mouse syngeneic CRC CMT93 and CT26 WT cell lines with stable mindin knock-down or overexpression. These cells were also subcutaneously injected into C57BL/6 and BALB/c mice as well as established a colitis-associated colorectal cancer (CAC) mouse model treated with lentiviral-based overexpression and knocked-down of mindin. Furthermore, we generated mindin knockout mice using a CRISPR-Cas9 system with CAC model. Our data showed that overexpression of mindin suppressed cell proliferation in both of CMT93 and CT26 WT colon cancer cell lines, while the silencing of mindin promoted in vitro cell proliferation via the ERK and c-Fos pathways and cell cycle control. Moreover, the overexpression of mindin significantly suppressed in vivo tumour growth in both the subcutaneous transplantation and the AOM/DSS-induced CAC models. Consistently, the silencing of mindin reversed these in vivo observations. Expectedly, the tumour growth was promoted in the CAC model on mindin-deficient mice. Thus, mindin plays a direct tumour suppressive function during colon cancer progression and suggesting that mindin might be exploited as a therapeutic target for CRC.

RevDate: 2020-07-02

Douglas AJ, Hug LA, BA Katzenback (2020)

Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure.

Microbial ecology pii:10.1007/s00248-020-01550-5 [Epub ahead of print].

While a number of amphibian skin microbiomes have been characterized, it is unclear how these communities might vary in response to seasonal changes in the environment and the corresponding behaviors that many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defense against pathogens, investigating how changes in the environment impact the microbial species present will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the bacterial skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the bacterial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether community composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon relative abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity; however, this may be due to our limited female frog sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs' respective pond water. Across seasons, diversity analyses suggest that there are significant differences between the bacterial skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.

RevDate: 2020-07-02

Van den Abbeele P, Verstrepen L, Ghyselinck J, et al (2020)

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.

Nutrients, 12(7): pii:nu12071917.

Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host-microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.

RevDate: 2020-07-01

Skarżyńska E, Wilczyńska P, Kiersztyn B, et al (2020)

Comparison of protease and aminopeptidase activities in meconium: A pilot study.

Biomedical reports, 13(2):7.

The successive accumulation of proteases and aminopeptidases in meconium are important physiological components of the intrauterine environment in which a fetus develops. The aim of the present study was to assess the changes in the activities of these enzymes in meconium of healthy infants, and to investigate whether there were any statistically significant associations between activity of the enzymes of interest and the mode of delivery. The activities of proteases and aminopeptidases were determined in meconium portions (n=110) using the substrates BODIPY FL casein and L-leucine-7-amido-4-methylcoumarin hydrochloride, respectively. Serial meconium samples (2-5 per neonate) were collected from healthy infants born vaginally (n=14), and by a cesarean section (n=16). Protease activity (104 RFU/h) was lower in the first meconium sample compared with the final sample from the same infant (3.99±2.03 vs. 5.76±2.24, respectively, mean ± standard deviation; P=0.004). Conversely, there was no significant difference in aminopeptidase activity (103 nM/l/h) between consecutive meconium samples (P=0.702). The ratios of the first-meconium sample enzyme activity to the last-meconium sample enzyme activity were lower for proteases compared with aminopeptidases (0.76±0.48 vs. 1.35±1.04, respectively mean ± standard deviation; P=0.014), and sustained in the infants born by a cesarean section (P=0.008). Spearman's correlation coefficient analysis between the first and last meconium samples showed the correlation increased in the infants born vaginally compared with the rest of the infants (proteases, R=0.618 vs. R=0.314; aminopeptidases, R=0.688 vs. R=0.566). Aminopeptidase activity did not exhibit any notable dynamic changes during meconium accumulation in the fetal intestine. In infants born vaginally compared with those born by a cesarean section, the activity of both proteases and aminopeptidases in the first meconium sample showed an improved correlation with the activity of the final meconium sample. This may suggest that in the intrauterine environment, during accumulation of meconium in the digestive tract of the fetus, the activity and/or levels of these enzymes and the substrates they catalyze were more stable in newborns born vaginally compared with infants born by caesarean section.

RevDate: 2020-07-01

Altamia MA, Lin Z, Trindade-Silva AE, et al (2020)

Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes.

mSystems, 5(3): pii:5/3/e00261-20.

Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites.IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.

RevDate: 2020-07-01

Berg G, Rybakova D, Fischer D, et al (2020)

Microbiome definition re-visited: old concepts and new challenges.

Microbiome, 8(1):103 pii:10.1186/s40168-020-00875-0.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

RevDate: 2020-06-29

Balan B, Dhaulaniya AS, Jamwal R, et al (2020)

Rapid detection and quantification of sucrose adulteration in cow milk using Attenuated total reflectance-Fourier transform infrared spectroscopy coupled with multivariate analysis.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 240:118628 pii:S1386-1425(20)30607-7 [Epub ahead of print].

Adulteration of milk to gain economic benefit has become a common practice in recent years. Sucrose is illegally added in milk to reconstitute its compositional requirement by improving the total solid contents. The present study is aimed to use FTIR spectroscopy in combination with multivariate chemometric modelling for the differentiation and quantification of sucrose in cow milk. Pure milk and adulterated milk spectra (0.5-7.5% w/v) were observed in the spectral region 4000-400 cm-1. Principal component analysis (PCA) was used for the discrimination of pure milk and adulterated milk. Soft independent modelling of class analogy (SIMCA) was able to classify test samples with a classification efficiency of 100%. Partial least square regression (PLS-R) and principle component regression (PCR) models were established for normal spectra, 1st derivative and 2nd derivative for the quantification of sucrose in milk. PLS-R model (normal spectra) in the combined wavenumber range of 1070-980 cm-1 showed the best prediction based on parameters like coefficient of determination (R2) (Cal: 0.996; Val: 0.993), RMSE (Cal: 0.15% w/v; Val: 0.20% w/v), RE% (Cal: 4.9% w/v; Val: 5.1% w/v) and RPD (13.40). This method has a detection level of 0.5% w/v sucrose adulteration.

RevDate: 2020-06-30

Hernández M, Planells P, Martínez E, et al (2020)

Microbiology of molar-incisor hypomineralization lesions. A pilot study.

Journal of oral microbiology, 12(1):1766166.

Objective: An insufficient mineralization (hypomineralization) in the teeth during the maturation stage of amelogenesis cause defects in 3-44% of children. Here, we describe for the first time the microbiota associated with these defects and compared it to healthy teeth within the same subjects. Methods: Supragingival dental plaque was sampled from healthy and affected teeth from 25 children with molar-incisor hypomineralization (MIH). Total DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing in order to describe the bacterial composition. Results: We detected a higher bacterial diversity in MIH samples, suggesting better bacterial adhesion or higher number of niches in those surfaces. We found the genera Catonella, Fusobacterium, Campylobacter, Tannerella, Centipeda, Streptobacillus, Alloprevotella and Selenomonas associated with hypomineralized teeth, whereas Rothia and Lautropia were associated with healthy sites. Conclusion: The higher protein content of MIH-affected teeth could favour colonization by proteolytic microorganisms. The over-representation of bacteria associated with endodontic infections and periodontal pathologies suggests that, in addition to promote caries development, MIH could increase the risk of other oral diseases.

RevDate: 2020-06-29

Morono Y, Kubota K, Tsukagoshi D, et al (2020)

EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples.

Microbes and environments, 35(3):.

Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.

RevDate: 2020-06-28

Sugden S, St Clair CC, LY Stein (2020)

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota.

Microbial ecology pii:10.1007/s00248-020-01547-0 [Epub ahead of print].

Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

RevDate: 2020-06-27

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

The interaction of dissolved organic nitrogen removal and microbial abundance in iron-filings based green environmental media for stormwater treatment.

Environmental research, 188:109815 pii:S0013-9351(20)30710-6 [Epub ahead of print].

Nonpoint sources pollution from agricultural crop fields and urbanized regions oftentimes have elevated concentrations of dissolved organic nitrogen (DON) in stormwater runoff, which are difficult for microbial communities to decompose. The impact of elevated DON can be circumvented through the use of green sorption media, such as Biosorption Activated Media (BAM) and Iron-Filing Green Environmental Media (IFGEM), which, as integral parts of microbial ecology, can contribute to the decomposition of DON. To compare the fate, transport, and transformation of DON in green sorption media relative to natural soil (control), a series of fixed-bed columns, which contain natural soil, BAM, and two types of IFGEM, respectively, were constructed to compare nutrient removal efficiency under three distinct stormwater influent conditions containing nitrogen and phosphorus. The interactions among six microbial species, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, complete ammonia oxidation (comammox) bacteria, anaerobic ammonium oxidation (anammox) bacteria, dissimilatory nitrate reduction to ammonium bacteria, and iron-reducing bacteria, were further analyzed from microbial ecology perspectives to determine the DON impact on nutrient removal in BAM and IFGEM. Natural soil was only able to achieve adequate DON transformation at the influent condition of lower nutrient concentration. However, the two types of IFGEM showed satisfactory nutrient removals and achieved greater transformation of DON relative to BAM when treating stormwater in all three influent conditions.

RevDate: 2020-06-27

Luo Y, Huang Y, Xu R, et al (2020)

Primary and secondary succession mediates the accumulation of biogenic amines during industrial semidry Chinese rice wine fermentation.

Applied and environmental microbiology pii:AEM.01177-20 [Epub ahead of print].

The exogenous functional microorganisms to regulate the biogenic amines (BAs) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference system, the BAs-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BAs-associated microbial functionality based on PICRUSt indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas and Enterobacter were prominently contributed to decarboxylase gene family in CRW. The expression level of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc) and agmatine deiminase gene (aguA) were assessed by q-PCR. The transcription levels of these genes are unmatched with BAs formation rate during post fermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference of CRW fermentation by co-inoculated Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) at a ratio of 1:2 exhibited the best synergetic control of BAs. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BAs-associated microbiota (|ρ|>0), Exiguobacterium and Pseudomonas were strongly suppress by Lactobacillus (P < 0.05, ρ = -0.867, ρ = -0.782), Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in co-inoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented the evidence for the obtained BAs-associated contributors. Overall, this work provides important insight into the microbial traits rely on resource usage and functional microbiota within food microbial ecology.Importance Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allows for determinations of taxonomic diversity, community traits and functional transformations over time or after a disturbance. The kinetics of BA generation, the patterns of resource consumption, functional metagenome prediction and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In the study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately lowered BA accumulation. Thus, this succession system could facilitate to settle essential issues with respect to microbial traits rely on resource usage and microbial interactions that occur in natural ecosystems.

RevDate: 2020-06-26

Zhou X, Wang JT, Wang WH, et al (2020)

Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici.

Microbial ecology pii:10.1007/s00248-020-01535-4 [Epub ahead of print].

Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.

RevDate: 2020-06-25

Mapelli F, Riva V, Vergani L, et al (2020)

Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere.

Microbial ecology pii:10.1007/s00248-020-01543-4 [Epub ahead of print].

The microbiota associated to xerophyte is a "black box" that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.

RevDate: 2020-06-25

Trego AC, Galvin E, Sweeney C, et al (2020)

Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development.

Frontiers in microbiology, 11:1126.

Methanogenic sludge granules are densely packed, small, spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. Each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion (AD) process. Information on exactly how methanogenic granules develop, and their eventual fate will be important for precision management of environmental biotechnologies. Granules from a full-scale bioreactor were size-separated into small (0.6-1 mm), medium (1-1.4 mm), and large (1.4-1.8 mm) size fractions. Twelve laboratory-scale bioreactors were operated using either small, medium, or large granules, or unfractionated sludge. After >50 days of operation, the granule size distribution in each of the small, medium, and large bioreactor sets had diversified beyond-to both bigger and smaller than-the size fraction used for inoculation. Interestingly, extra-small (XS; <0.6 mm) granules were observed, and retained in all of the bioreactors, suggesting the continuous nature of granulation, and/or the breakage of larger granules into XS bits. Moreover, evidence suggested that even granules with small diameters could break. "New" granules from each emerging size were analyzed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae, and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration (MINT) analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules.

RevDate: 2020-06-25

Navarro MOP, Dilarri G, Simionato AS, et al (2020)

Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.

Frontiers in microbiology, 11:1076.

The antibiotic activity of metalloantibiotic compounds has been evaluated since the 90s, and many different modes of action were characterized. In the last decade, the effects of secondary metabolites produced by Pseudomonas aeruginosa LV strain, including a cupric compound identified as Fluopsin C, were tested against many pathogenic bacteria strains, proving their high antibiotic activity. In the present study, the bactericidal mechanisms of action of Fluopsin C and the semi-purified fraction F4A were elucidated. The results found in electron microscopy [scanning electron microscopy (SEM) and transmission electronic microscopy (TEM)] demonstrated that both Fluopsin C and F4A are affecting the cytoplasmatic membrane of Gram-positive and Gram-negative bacteria. These results were confirmed by fluorescence microscopy, where these bacteria presented permeabilization of their cytoplasmatic membranes after contact with the semi-purified fraction and pure compound. Using electronic and fluorescence microscopy, along with bacterial mutant strains with marked divisional septum, the membrane was defined as the primary target of Fluopsin C in the tested bacteria.

RevDate: 2020-06-25

Gill AS, Purnell K, Palmer MI, et al (2020)

Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types.

Frontiers in microbiology, 11:912.

Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.

RevDate: 2020-06-25

Garber A, Hastie PM, Farci V, et al (2020)

The effect of supplementing pony diets with yeast on 2. The faecal microbiome.

Animal : an international journal of animal bioscience pii:S1751731120001512 [Epub ahead of print].

There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.

RevDate: 2020-06-24

Huang R, Zeng J, Zhao D, et al (2020)

Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes.

Microbial ecology pii:10.1007/s00248-020-01545-2 [Epub ahead of print].

Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH4+-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.

RevDate: 2020-06-24

Lopetuso LR, Quagliariello A, Schiavoni M, et al (2020)

Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.

Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver pii:S1590-8658(20)30225-5 [Epub ahead of print].

BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.

AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.

METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.

RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with α-diversity.

CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.

RevDate: 2020-06-23

Desai C, Handley SA, Rodgers R, et al (2020)

Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children.

PLoS neglected tropical diseases, 14(6):e0008387 pii:PNTD-D-19-01316.

Environmental enteric dysfunction (EED) is characterized by diffuse villous atrophy of the small bowel. EED is strongly associated with stunting, a major public health problem linked to increased childhood morbidity and mortality. EED and subsequent stunting of linear growth are surmised to have microbial origins. To interrogate this relationship, we defined the comprehensive virome (eukaryotic virus and bacteriophage) and bacterial microbiome of a longitudinal cohort of rural Malawian children with extensive metadata and intestinal permeability testing at each time point. We found thirty bacterial taxa differentially associated with linear growth. We detected many eukaryotic viruses. Neither the total number of eukaryotic families nor a specific viral family was statistically associated with improved linear growth. We identified 3 differentially abundant bacteriophage among growth velocities. Interestingly, there was a positive correlation between bacteria and bacteriophage richness in children with subsequent adequate/moderate growth which children with subsequent poor growth lacked. This suggests that a disruption in the equilibrium between bacteria and bacteriophage communities might be associated with subsequent poor growth. Future studies of EED and stunting should include the evaluation of viral communities in addition to bacterial microbiota to understand the complete microbial ecology of these poorly understood entities.

RevDate: 2020-06-23

Díaz-García L, Bugg TDH, DJ Jiménez (2020)

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.

Microbial ecology pii:10.1007/s00248-020-01546-1 [Epub ahead of print].

An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.

RevDate: 2020-06-23

Cohen H, McFrederick QS, SM Philpott (2020)

Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria : RRH: Environmental Drivers of Bee Microbiome.

Microbial ecology pii:10.1007/s00248-020-01549-y [Epub ahead of print].

Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.

RevDate: 2020-06-23

Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, et al (2020)

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.

Microbial ecology pii:10.1007/s00248-020-01530-9 [Epub ahead of print].

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L-1, iron ~ 35-61 mg L-1 (waters), and ~ 8-293 g kg-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

RevDate: 2020-06-23

Li L, Wang S, Wang H, et al (2020)

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.

Nature ecology & evolution pii:10.1038/s41559-020-1221-7 [Epub ahead of print].

Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.

RevDate: 2020-06-23

Ren FR, Sun X, Wang TY, et al (2020)

Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits.

The ISME journal pii:10.1038/s41396-020-0704-5 [Epub ahead of print].

Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.

RevDate: 2020-06-22

Toe LC, Kerckhof FM, De Bodt J, et al (2020)

A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants.

FEMS microbiology ecology, 96(7):.

Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.

RevDate: 2020-06-20

Rowles Iii LS, Hossain AI, Ramirez I, et al (2020)

Seasonal contamination of well-water in flood-prone colonias and other unincorporated U.S. communities.

The Science of the total environment, 740:140111 pii:S0048-9697(20)33632-9 [Epub ahead of print].

Many of the six million residents of unincorporated communities in the United States depend on well-water to meet their needs. One group of unincorporated communities is the colonias, located primarily in several southwestern U.S. states. Texas is home to the largest number of these self-built communities, of mostly low-income families, lacking basic infrastructure. While some states have regulations that mandate minimum infrastructure for these communities, water and sewage systems are still lacking for many of their residents. Unprotected wells and self-built septic/cesspool systems serve as the primary infrastructure for many such colonias. This research was designed to probe how wells and septic/cesspool systems are influenced by heavy rainfall events. Such events are hypothesized to impact water quality with regard to human health. Inorganic and microbiological water quality of the wells in nine colonias located in Nueces County, Texas, were evaluated during dry and wet periods. Nueces County was selected as an example based on its flooding history and the fact that many colonias there depend entirely on well-water and septic/cesspool systems. The results demonstrate that well-water quality in these communities varies seasonally with respect to arsenic (up to 35 μg/L) and bacterial contamination (Escherichia coli), dependent on the amount of rainfall, which leaves this population vulnerable to health risks during both wet and dry periods. Microbial community analyses were also conducted on selected samples. To explore similar seasonal contamination of well-water, an analysis of unincorporated communities, flooding frequency, and arsenic contamination in wells was conducted by county throughout the United States. This nationwide analysis indicates that unincorporated communities elsewhere in the United States are likely experiencing comparable challenges for potable water access because of a confluence of socioeconomic, infrastructural, and policy realities.

RevDate: 2020-06-20

Rapp D, Ross CM, Maclean P, et al (2020)

Investigation of On-Farm Transmission Routes for Contamination of Dairy Cows with Top 7 Escherichia coli O-Serogroups.

Microbial ecology pii:10.1007/s00248-020-01542-5 [Epub ahead of print].

Shiga toxin-producing Escherichia coli (STEC) are foodborne bacterial pathogens, with cattle a significant reservoir for human infection. This study evaluated environmental reservoirs, intermediate hosts and key pathways that could drive the presence of Top 7 STEC (O157:H7, O26, O45, O103, O111, O121 and O145) on pasture-based dairy herds, using molecular and culture-based methods. A total of 235 composite environmental samples (including soil, bedding, pasture, stock drinking water, bird droppings and flies and faecal samples of dairy animals) were collected from two dairy farms, with four sampling events on each farm. Molecular detection revealed O26, O45, O103 and O121 as the most common O-serogroups, with the greatest occurrence in dairy animal faeces (> 91%), environments freshly contaminated with faeces (> 73%) and birds and flies (> 71%). STEC (79 isolates) were a minor population within the target O-serogroups in all sample types but were widespread in the farm environment in the summer samplings. Phylogenetic analysis of whole genome sequence data targeting single nucleotide polymorphisms revealed the presence of several clonal strains on a farm; a single STEC clonal strain could be found in several sample types concurrently, indicating the existence of more than one possible route for transmission to dairy animals and a high rate of transmission of STEC between dairy animals and wildlife. Overall, the findings improved the understanding of the ecology of the Top 7 STEC in open farm environments, which is required to develop on-farm intervention strategies controlling these zoonoses.

RevDate: 2020-06-20

Adomako MO, Xue W, Tang M, et al (2020)

Synergistic Effects of Soil Microbes on Solidago canadensis Depend on Water and Nutrient Availability.

Microbial ecology pii:10.1007/s00248-020-01537-2 [Epub ahead of print].

Soil microbes may greatly affect plant growth. While plants are commonly associated with diverse communities of soil microbes, complementary roles of different microbial communities that may stimulate synergistic effects on plant growth are not adequately tested. Also, such synergistic effects may vary with environmental conditions such as soil nutrient and water availability. We conducted a greenhouse experiment with a widespread clonal plant Solidago canadensis. The experiment was a factorial design with four levels of soil microbial inoculation (fresh soil inocula from grasslands in northern and southern China that were expected to differ in soil microbial composition, a mixture of the two fresh soil inocula, and a sterilized mixed inoculum control), two levels of nutrient availability (low vs. high), and two levels of water supply (low vs. high, i.e., 1376 vs. 352 mm per year). Irrespective of water supply and nutrient availability, total, aboveground, and belowground mass of S. canadensis were generally higher when the plant grew in soil inoculated with a mixture of soil microbes from the south and north of China (in the mixed inoculum treatment) than when it grew in soil inoculated with soil microbes from only the north or the south or the sterilized control. Such effects of soil microbes on total and aboveground mass were stronger under high than under low nutrient availability and also under high than under low water supply. Our results suggest that interactions of different soil microbial communities can result in a synergistic effect on plant growth and such a synergistic effect depends on environmental conditions. The findings shed light on the importance of plant-microbe interactions during the spreading of some plant species in face of increased atmospheric nutrient deposition coupled with altered rainfall pattern due to global change.

RevDate: 2020-06-20

Blackwell N, Bryce C, Straub D, et al (2020)

Genomic insights into two novel Zetaproteobacteria Fe(II)-oxidizing isolates reveal lifestyle adaption to coastal marine sediments.

Applied and environmental microbiology pii:AEM.01160-20 [Epub ahead of print].

The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular-based techniques demonstrating their global distribution, relatively few isolates exist, especially from low Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here we present the genomes (>99% genome completeness) of two Zetaproteobacteria which are the only cultivated isolates originating from typical, low Fe (porewater Fe(II) 70-100 μM) coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other, and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were M. aestuarium CP-5 and M. ferrinatatus CP-8 (96-98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations indicated by the presence of both cbb3 - and aa3 -type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.Importance Until recently, the importance and relevance of Zetaproteobacteria was mainly thought to be restricted to high Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical, low Fe(II), coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation, and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II)-oxidizers.

RevDate: 2020-06-20

Onyango SO, De Clercq N, Beerens K, et al (2020)

Oral microbiota display profound differential metabolic kinetics and community shifts upon incubation with sucrose, trehalose, kojibiose and xylitol.

Applied and environmental microbiology pii:AEM.01170-20 [Epub ahead of print].

This study compares the metabolic properties of kojibiose, trehalose, sucrose and xylitol upon incubation with representative oral bacteria as monocultures, synthetic communities or with human salivary bacteria in a defined medium. As compared to sucrose and trehalose, kojibiose resisted metabolism during a 48h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus spp. based communities, as well as salivary bacteria displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15 respectively that are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted and differences in pH drop during incubation indicated different rates of sugar metabolism. Yet, functional analysis indicated lactate, acetate and formate to evenly dominate the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that significant shift of microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. Streptococcus spp. a taxon linked to cariogenesis dominated in sucrose (91.8±6.4%) and trehalose (55.9±38.6%) representing a high diversity loss. In contrast, Streptococcus (5.1±3.7%) was less abundant in kojibiose which instead was dominated by Veillonella (26.8±19.6%) while for xylitol Neisseria (29.4±19.1%) was most abundant. Overall, kojibiose and xylitol incubations less stimulated cariogenic species yet closely maintained an abundance of key phyla and genera of salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide; kojibiose whose mass production methodology has recently been made possible. While the resistance of kojibiose was established with monocultures, a delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is therefore, less metabolizable as compared to sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization, this is in sharp contrast with tests that solely rely on monocultures such as S. mutans, which clearly fail to capture complex interaction between oral microbiota.

RevDate: 2020-06-19

Prudence SMM, Addington E, Castaño-Espriu L, et al (2020)

Advances in actinomycete research: an ActinoBase review of 2019.

Microbiology (Reading, England) [Epub ahead of print].

The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.

RevDate: 2020-06-19

Fuster M, Billard H, Mandart M, et al (2020)

Trophic Conditions Influence Widespread Distribution of Aster-Like Nanoparticles Within Aquatic Environments.

Microbial ecology pii:10.1007/s00248-020-01541-6 [Epub ahead of print].

Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r2 = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 106 ALNs mL-1) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.

RevDate: 2020-06-19

Carteron A, Beigas M, Joly S, et al (2020)

Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.

Microbial ecology pii:10.1007/s00248-020-01540-7 [Epub ahead of print].

In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.

RevDate: 2020-06-19

Coil DA, Neches RY, Lang JM, et al (2020)

Bacterial communities associated with cell phones and shoes.

PeerJ, 8:e9235 pii:9235.

Background: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively.

Findings: We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States.

Conclusions: We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of "environmental" taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.

RevDate: 2020-06-19

LaSarre B, Deutschbauer AM, Love CE, et al (2020)

Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism.

Applied and environmental microbiology, 86(13): pii:AEM.00543-20.

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4+ The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a prioriIMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

RevDate: 2020-06-17

Rantsiou K, Giacosa S, Pugliese M, et al (2020)

Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest.

Frontiers in plant science, 11:700.

Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.

RevDate: 2020-06-17

Gulino K, Rahman J, Badri M, et al (2020)

Initial Mapping of the New York City Wastewater Virome.

mSystems, 5(3): pii:5/3/e00876-19.

Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

RevDate: 2020-06-16

Cahill N, D Morris (2020)

Recreational waters - A potential transmission route for SARS-CoV-2 to humans?.

The Science of the total environment, 740:140122 pii:S0048-9697(20)33643-3 [Epub ahead of print].

Coronavirus disease 2019 (COVID-19), the respiratory illness caused by the novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has lead to high morbidity and mortality rates worldwide, has been causing major public health concerns since first detected in late 2019. Following identification of novel pathogens, questions in relation to dissemination of the pathogen and transmission routes begin to emerge. This rapidly spreading SARS-CoV-2 virus has been detected in both faecal and wastewater samples across the globe, highlighting the potential for faecal-oral transmission of the virus. As a result, concerns regarding the transmission of the virus in the environment and the risk associated with contracting the virus in recreational waters, particularly where inadequately treated wastewater is discharged, have been emerging in recent weeks. This paper highlights the need for further research to be carried out to investigate the presence, infectivity and viability of this newly identified SARS-CoV-2 virus in wastewater effluent and receiving recreational waters.

RevDate: 2020-06-16

Candry P, Ulcar B, Petrognani C, et al (2020)

Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities.

Bioresource technology pii:S0960-8524(20)30923-8 [Epub ahead of print].

Microbial production of valerate, a five-carbon carboxylate, can occur from propionate and ethanol through a process called odd-chain elongation. The generation of even-chain compounds in this process lowers product selectivity, forming a key challenge. This study investigated factors determining product selectivity during odd-chain elongation in an odd-chain elongating mixed community and the pure culture Clostridium kluyveri DSM555. Incubations at different ratios of ethanol:propionate showed that increasing ratios (from 0.5 to 7) lowered product specificity, as evidenced by a decrease in the odd:even product ratio from 5.5 to 1.5 for C. kluyveri and from 15 to 0.8 for the mixed community. The consistency of these observations with literature data suggests that control of ethanol:propionate ratio offers a robust tool for process control in odd-chain elongation, while the flexible metabolism can also have implications for efficient use of ethanol during even-chain elongation processes.

RevDate: 2020-06-16

Zagdoun M, Coeuret G, N'Dione M, et al (2020)

Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps.

Food microbiology, 91:103547.

Cooked ham production involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O2 packaging permeability. About 200 samples from the same facility were obtained and characterized with respect to i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to d-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O2-permeable packaging. Within a given slicing line, campaign-based variations were observed, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with l-lactic acid production and C. maltaromaticum with formic and acetic acid productions.

RevDate: 2020-06-15

Hussan JR, PJ Hunter (2020)

Our natural "makeup" reveals more than it hides: Modeling the skin and its microbiome.

Wiley interdisciplinary reviews. Systems biology and medicine [Epub ahead of print].

Skin is our primary interface with the environment. A structurally and functionally complex organ that hosts a dynamic ecosystem of microbes, and synthesizes many compounds that affect our well-being and psychosocial interactions. It is a natural platform of signal exchange between internal organs, skin resident microbes, and the environment. These interactions have gained a great deal of attention due to the increased prevalence of atopic diseases, and the co-occurrence of multiple allergic diseases related to allergic sensitization in early life. Despite significant advances in experimentally characterizing the skin, its microbial ecology, and disease phenotypes, high-levels of variability in these characteristics even for the same clinical phenotype are observed. Addressing this variability and resolving the relevant biological processes requires a systems approach. This review presents some of our current understanding of the skin, skin-immune, skin-neuroendocrine, skin-microbiome interactions, and computer-based modeling approaches to simulate this ecosystem in the context of health and disease. The review highlights the need for a systems-based understanding of this sophisticated ecosystem. This article is categorized under: Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models Laboratory Methods and Technologies > Metabolomics Physiology > Organismal Responses to Environment.

RevDate: 2020-06-14

Cardarelli EL, Bargar JR, CA Francis (2020)

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.

Microbial ecology pii:10.1007/s00248-020-01534-5 [Epub ahead of print].

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

RevDate: 2020-06-12

López-López A, A Mira (2020)

Shifts in Composition and Activity of Oral Biofilms After Fluoride Exposure.

Microbial ecology pii:10.1007/s00248-020-01531-8 [Epub ahead of print].

Oral diseases are biofilm-mediated diseases caused by imbalances in the ecology of resident microflora. Among them, dental caries (tooth decay) is considered the most common disease worldwide, and toothbrushing, which physically eliminates the oral biofilm, is the most widespread prevention strategy. Although it is well established that fluoride increases enamel resistance to acidic pH and promotes tooth remineralization, its effect on the biofilm bacterial communities' composition and metabolism is not fully understood. We have grown in vitro oral biofilms and used 16S rRNA Illumina sequencing to study the effect of fluoride on DNA- and RNA-based bacterial populations. In addition, a metatranscriptomic approach has also been performed, in which total RNA has been sequenced to study gene expression profiles in the presence/absence of 500 ppm sodium fluoride. Our data show a lower pH drop and a clear shift in total and metabolically active bacterial composition after fluoride exposure. Streptococcus oralis was the species most affected, with a 10-fold reduction in both DNA and RNA samples, whereas Rothia mucilaginosa underwent an 8-fold increase in the DNA and S. salivarius a 4- and 5-fold increase in the RNA and DNA samples, respectively. The metatranscriptomes indicated that fluoride exposure induced a dramatic shutdown of sugar metabolism, including significant under-expression of different sugar transporters, fucosidases, and a pyruvate oxidase, among others. The reduction in saccharolytic organisms and the inhibition of sugar fermentation pathways by fluoride may therefore be considered instrumental for the beneficial effect of fluoride-containing oral hygiene products.

RevDate: 2020-06-11

Aszalós JM, Szabó A, Megyes M, et al (2020)

Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region).

Astrobiology, 20(6):754-765.

Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.

RevDate: 2020-06-11

Verbeeck K, De Vrieze J, Pikaar I, et al (2020)

Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production.

Microbial biotechnology [Epub ahead of print].

Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.

RevDate: 2020-06-11

Taparia T, Krijger M, Hodgetts J, et al (2020)

Six Multiplex TaqManTM-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms.

Frontiers in microbiology, 11:989.

Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqManTM assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: "Pseudomonas gingeri," Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.

RevDate: 2020-06-10

Topçuoğlu BD, Lesniak NA, Ruffin MT, et al (2020)

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.

mBio, 11(3): pii:mBio.00434-20.

Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.

RevDate: 2020-06-09

Koch C, Kuchenbuch A, Marosvölgyi M, et al (2020)

Label-free four-dimensional visualization of anaerobically growing electroactive biofilms.

Cytometry. Part A : the journal of the International Society for Analytical Cytology [Epub ahead of print].

Light sheet fluorescence microscopy (LSFM) allows non-destructive, label-free and in vivo imaging of large specimen, even at non-transparent surfaces. We show that LSFM can be applied for label-free analyses of prokaryotes on the example of electroactive biofilms. Biofilm growth is linked to the production of current serving as measure of metabolic activity in vivo by monitoring with high spatial and temporal resolution. After 35 h of exponential growth a homogeneous biofilm with a thickness of 9 μm was formed. This was followed by a stratification of the biofilm including formation of 3D structures over the next 100 h. Light reflection was sufficient to visualize the biofilm structure and development over time and the terminal morphology was confirmed using fluorescence staining. This proof of concept on using LSFM for investigation of biofilms opens the door for its application in the entire field of microbial ecology.

RevDate: 2020-06-09

McGee CF (2020)

The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks.

Environmental science and pollution research international pii:10.1007/s11356-020-09548-9 [Epub ahead of print].

The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.

RevDate: 2020-06-09

Ruan Y, Wang T, Guo S, et al (2020)

Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages.

Microbial ecology pii:10.1007/s00248-020-01532-7 [Epub ahead of print].

Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.

RevDate: 2020-06-09

Murray AE, Freudenstein J, Gribaldo S, et al (2020)

Roadmap for naming uncultivated Archaea and Bacteria.

Nature microbiology pii:10.1038/s41564-020-0733-x [Epub ahead of print].

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

RevDate: 2020-06-08

Di Cesare A, Pjevac P, Eckert E, et al (2020)

The role of metal contamination in shaping microbial communities in heavily polluted marine sediments.

Environmental pollution (Barking, Essex : 1987), 265(Pt B):114823 pii:S0269-7491(20)31759-0 [Epub ahead of print].

Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.

RevDate: 2020-06-08

Gurney J, Azimi S, Brown SP, et al (2020)

Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies.

Microbiology (Reading, England) [Epub ahead of print].

In the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing (QS) is a social trait that is exploitable by non-cooperating cheats. Previously it has been shown that by linking QS to the production of both public and private goods, cheats can be prevented from invading populations of cooperators and this was described by Dandekar et al. (Science 2012;338:264-266) as 'a metabolic incentive to cooperate'. We hypothesized that P. aeruginosa could evolve novel cheating strategies to circumvent private goods metabolism by rewiring its combinatorial response to two QS signals (3O-C12-HSL and C4-HSL). We performed a selection experiment that cycled P. aeruginosa between public and private goods growth media and evolved an isolate that rewired its control of cooperative protease expression from a synergistic (AND-gate) response to dual-signal input to a 3O-C12-HSL-only response. We show that this isolate circumvents metabolic incentives to cooperate and acts as a combinatorial signalling cheat, with higher fitness in competition with its ancestor. Our results show three important principles: first, combinatorial QS allows for diverse social strategies to emerge; second, restrictions levied by private goods are not sufficient to explain the maintenance of cooperation in natural populations; and third, modifying combinatorial QS responses could result in important physiological outcomes in bacterial populations.

RevDate: 2020-06-08

Iddins BO, Waugh MH, Robbins T, et al (2020)

Antimicrobial Silver Touch Surfaces in an Occupational Medicine Clinic.

Journal of occupational and environmental medicine, 62(6):e287-e288.

RevDate: 2020-06-08

Chopra S, D Kumar (2020)

Ibuprofen as an emerging organic contaminant in environment, distribution and remediation.

Heliyon, 6(6):e04087 pii:e04087.

Pharmaceutical and personal care products (PPCPs) are the one of sub-class under emerging organic contaminants (EOCs). Ibuprofen is the world's third most consumable drug. This drug enters into our water system through human pharmaceutical use. It attracts the attention of environmentalist on the basis of risk associated, presence and transformation in the environment. The detection and removal are the two key area where we need to focus. The concentration of such compounds in waterbodies detected through conventional and also by the advanced methods. This review we described the available technologies including chemical, physical and biological methods, etc used the for removal of Ibuprofen. The pure culture based method, mixed culture approach and activated sludge culture approach focused and pathway of degradation of ibuprofen was deciphered by using the various methods of structure determination. The various degradation methods used for Ibuprofen are discussed. The advanced methods coupled with physical, chemical, biological, chemical methods like ozonolysis, oxidation and adsorption, nanotechnology based methods, nanocatalysis and use of nonosensors to detect the presence of small amount in waterbodies can enhance the future degradation of this drug. It is necessary to develop the new detection methods to enhance the detection of such pollutants. With the developments in new detection methods based on GC-MS//MS, HPLC, LC/MS and nanotechnology based sensors makes easier detection of these compounds which can detect even very minute amount with great sensitivity and in less time. Also, the isolation and characterization of more potent microbial strains and nano-photocatalysis will significantly increase the future degradation of such harmful compounds from the environment.

RevDate: 2020-06-08

Mercer KE, Yeruva L, Pack L, et al (2020)

Xenometabolite signatures in the UC Davis Type 2 Diabetes Mellitus Rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.

American journal of physiology. Gastrointestinal and liver physiology [Epub ahead of print].

The gut microbiome has the potential to create or modify xenometabolites (i.e., non-host derived metabolites) through de novo synthesis or modification of exogenous and endogenous compounds. While there are isolated examples of xenometabolites influencing host health and disease, wide-scale characterization of these metabolites remain limited. We developed a metabolomics platform ("XenoScan") using liquid chromatography-mass spectrometry to characterize a range of known and suspected xenometabolites and their derivatives. This assay currently applies authentic standards for 189 molecules, enriched for metabolites of microbial origin. As a proof-of-principle, we characterized the cecal content xenometabolomics profile in adult male lean Sprague Dawley (LSD) and UC Davis Type 2 Diabetes Mellitus (UCD-T2DM) Rats at different stages of diabetes. These results were correlated to specific bacterial species generated via shotgun metagenomic sequencing. UCD-T2DM rats had a unique xenometabolite profile compared with LSD rats, regardless of diabetes status. Furthermore, modeling approaches revealed that several xenometabolites discriminated UCD-T2DM rats with early-onset of diabetes vs. those at 3 months post-diabetes onset. Several xenometabolite hubs correlated with specific bacterial species in both LSD and UCD-T2DM rats. For example, indole-3-propionic acid negatively correlated with species within the Oscillibacter genus in UCD-T2DM rats with early onset of diabetes, in contrast to gluconic acid and trimethylamine that were positively correlated with Oscillibacter species. The application of a xenometabolite-enriched metabolomics assay in relevant milieus will enable rapid identification of a wide variety of gut-derived metabolites, their derivatives, and their potential biochemical origins of xenometabolites in relationship to host GI microbial ecology.

RevDate: 2020-06-06

Lacalle RG, Garbisu C, JM Becerril (2020)

Effects of the application of an organic amendment and nanoscale zero-valent iron particles on soil Cr(VI) remediation.

Environmental science and pollution research international pii:10.1007/s11356-020-09449-x [Epub ahead of print].

Chromium is considered an environmental pollutant of much concern whose toxicity depends, to a great extent, on its valence state, with Cr(VI) being more soluble, bioavailable, and toxic, compared to Cr(III). Nanoremediation is a promising strategy for the remediation of metal pollutants by changing their valence state. However, among other aspects, its effectiveness for soil remediation is seriously hampered by the interaction of nanoparticles with soil organic matter. In this study, soil was (i) amended with two doses of a municipal solid organic waste and (ii) artificially polluted with 300 mg Cr(VI) kg-1 DW soil. After a period of aging, a nanoremediation treatment with nanoscale zero-valent iron particles (1 g nZVI kg-1 DW soil) was applied. The efficiency of the remediation treatment was assessed in terms of Cr(VI) immobilization and recovery of soil health. The presence of the organic amendment caused (i) a decrease of redox potential, (ii) Cr(VI) immobilization via its reduction to Cr(III), (iii) a stimulation of soil microbial communities, and (iv) an improvement of soil health, compared to unamended soil. By contrast, nZVI did not have any impact on Cr(VI) immobilization nor on soil health. It was concluded that, unlike the presence of the organic amendment, nanoremediation with nZVI was not a valid option for soils polluted with Cr(VI) under our experimental conditions.

RevDate: 2020-06-06

Tao X, Feng J, Yang Y, et al (2020)

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.

Microbiome, 8(1):84 pii:10.1186/s40168-020-00838-5.

BACKGROUND: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.

RESULTS: The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.

CONCLUSIONS: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.

RevDate: 2020-06-05

Lu GS, LaRowe DE, Fike DA, et al (2020)

Bioenergetic characterization of a shallow-sea hydrothermal vent system: Milos Island, Greece.

PloS one, 15(6):e0234175 pii:PONE-D-19-30282.

Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔGr) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO2- (-136 to -162 kJ/mol e-), followed by reactions in which the electron acceptor/donor pairs were O2/CO, NO3-/CO, and NO2-/H2S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S0 oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S0 or H2S as electron donors and NO2- or O2 as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.

RevDate: 2020-06-05

Lee JC, KS Whang (2020)

Sphingomonas segetis sp. nov., isolated from spinach farming field soil.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 T (98.0 %), Sphingomonas agri HKS-06T (97.7 %) and Sphingomonas lutea JS5T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).

RevDate: 2020-06-05

Yang Y, Liu W, Zhang Z, et al (2020)

Microplastics provide new microbial niches in aquatic environments.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10704-x [Epub ahead of print].

Microplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase.Key Points• Bacteria are mainly studied in community analyses: fungi are neglected.• Microbial colonization of microplastics depends on substrate, location and time.• Community ecology is a promising approach to investigate microbial colonization.• Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.

RevDate: 2020-06-05

Hallin S, PLE Bodelier (2020)

Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry.

Frontiers in microbiology, 11:981.

RevDate: 2020-06-05

Liu W, Graham EB, Zhong L, et al (2020)

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability.

Frontiers in microbiology, 11:873.

Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.

RevDate: 2020-06-05

Benidire L, El Khalloufi F, Oufdou K, et al (2020)

Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network.

The Science of the total environment, 729:139020.

Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.

RevDate: 2020-06-05

Young JN, K Schmidt (2020)

It's what's inside that matters: physiological adaptations of high-latitude marine microalgae to environmental change.

The New phytologist [Epub ahead of print].

Marine microalgae within seawater and sea ice fuel high-latitude ecosystems and drive biogeochemical cycles through the fixation and export of carbon, uptake of nutrients, and production and release of oxygen and organic compounds. High-latitude marine environments are characterized by cold temperatures, dark winters and a strong seasonal cycle. Within this environment a number of diverse and dynamic habitats exist, particularly in association with the formation and melt of sea ice, with distinct microalgal communities that transition with the season. Algal physiology is a crucial component, both responding to the dynamic environment and in turn influencing its immediate physicochemical environment. As high-latitude oceans shift into new climate regimes the analysis of seasonal responses may provide insights into how microalgae will respond to long-term environmental change. This review discusses recent developments in our understanding of how the physiology of high-latitude marine microalgae is regulated over a polar seasonal cycle, with a focus on ice-associated (sympagic) algae. In particular, physiologies that impact larger scale processes will be explored, with an aim to improve our understanding of current and future ecosystems and biogeochemical cycles.

RevDate: 2020-06-04

Van den Abbeele P, Duysburgh C, Rakebrandt M, et al (2020)

Dried Yeast Cell Walls High in Beta-Glucan and Mannan-Oligosaccharides Positively Affect Microbial Composition and Activity in the Canine Gastrointestinal Tract in Vitro.

Journal of animal science pii:5851475 [Epub ahead of print].

The outer cell wall of yeast is characterized by high levels of β-glucans and mannan-oligosaccharides (MOS), which have been linked with beneficial effects on intestinal health and immune status in dogs. In this study, a standardized in vitro simulation of the canine gastrointestinal tract (Simulator of the Canine Intestinal Microbial Ecosystem; SCIME™) was used to evaluate the effect of a Saccharomyces cerevisiae-based product, consisting of 27.5% β-glucans and 22.5% MOS, on the activity (as assessed by measurement of fermentative metabolites) and composition (as assessed by 16S-targeted Illumina sequencing) of canine intestinal microbiota. The Saccharomyces cerevisiae-based product was tested at 3 different dosages, i.e. 0.5 g/day, 1.0 g/day and 2.0 g/day. A dose-dependent fermentation pattern was observed along the entire length of the colon, as shown by the increased production of the health-related acetate, propionate and butyrate for the three concentrations tested (0.5, 1.0 and 2.0 g/day). A consistent finding for all three tested concentrations was the increased propionate production (p<0.05) in the simulated proximal and distal colon. These changes in terms of fermentative metabolites could be linked to specific microbial alterations at family level, such as the specific stimulation of the propionate-producing families Porphyromonadaceae and Prevotellaceae upon in vitro exposure to the Saccharomyces cerevisiae-based product. Other consistent changes in community composition upon repeated exposure included the decrease in the Enterobacteriaceae and the Fusobacteriaceae families, which both contain several potentially opportunistic pathogens. Altogether, the generated data support a possible health-promoting role of a product high in β-glucans and MOS when supplemented to the dogs' diet.

RevDate: 2020-06-04

Xiong J, Li X, Yan M, et al (2020)

Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged.

Microbial ecology pii:10.1007/s00248-020-01533-6 [Epub ahead of print].

Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.

RevDate: 2020-06-04

Monteiro DA, Fonseca EDS, Rodrigues RAR, et al (2020)

Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase.

Scientific reports, 10(1):9075 pii:10.1038/s41598-020-66004-x.

Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.

RevDate: 2020-06-03

Semiatizki A, Weiss B, Bagim S, et al (2020)

Effects, interactions, and localization of Rickettsia and Wolbachia in the house fly parasitoid, Spalangia endius.

Microbial ecology pii:10.1007/s00248-020-01520-x [Epub ahead of print].

Many insect species harbor facultative microbial symbionts that affect their biology in diverse ways. Here, we studied the effects, interactions, and localization of two bacterial symbionts-Wolbachia and Rickettsia-in the parasitoid Spalangia endius. We crossed between four S. endius colonies-Wolbachia only (W), Rickettsia only (R), both (WR), and none (aposymbiotic, APS) (16 possible crosses) and found that Wolbachia induces incomplete cytoplasmic incompatibility (CI), both when the males are W or WR. Rickettsia did not cause reproductive manipulations and did not rescue the Wolbachia-induced CI. However, when R females were crossed with W or WR males, significantly less offspring were produced compared with that of control crosses. In non-CI crosses, the presence of Wolbachia in males caused a significant reduction in offspring numbers. Females' developmental time was significantly prolonged in the R colony, with adults starting to emerge one day later than the other colonies. Other fitness parameters did not differ significantly between the colonies. Using fluorescence in situ hybridization microscopy in females, we found that Wolbachia is localized alongside Rickettsia inside oocytes, follicle cells, and nurse cells in the ovaries. However, Rickettsia is distributed also in muscle cells all over the body, in ganglia, and even in the brain.

RevDate: 2020-06-03

Hejduková E, Elster J, L Nedbalová (2020)

Annual Cycle of Freshwater Diatoms in the High Arctic Revealed by Multiparameter Fluorescent Staining.

Microbial ecology pii:10.1007/s00248-020-01521-w [Epub ahead of print].

Diatoms (Bacillariophyceae) are important primary producers in a wide range of hydro-terrestrial habitats in polar regions that are characterized by many extreme environmental conditions. Nevertheless, how they survive periods of drought and/or freeze remains unknown. A general strategy of microorganisms to overcome adverse conditions is dormancy, but morphologically distinct diatom resting stages are rare. This study aimed to evaluate the annual cycle of freshwater diatoms in the High Arctic (Central Spitsbergen) and provide an insight into their physiological cell status variability. The diversity and viability of diatom cells were studied in samples collected five times at four study sites, tracing the key events for survival (summer vegetative season, autumn dry-freezing, winter freezing, spring melting, summer vegetative season [again]). For viability evaluation, a multiparameter fluorescent staining was used in combination with light microscopy and allowed to reveal the physiological status at a single-cell level. The proportions of the cell categories were seasonally and locality dependent. The results suggested that a significant portion of vegetative cells survive winter and provide an inoculum for the following vegetative season. The ice thickness significantly influenced spring survival. The thicker the ice layer was, the more dead cells and fewer other stages were observed. The influence of the average week max-min temperature differences in autumn and winter was not proven.

RevDate: 2020-06-03

Aliyu H, Mohr T, Cowan D, et al (2020)

Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air.

International journal of molecular sciences, 21(11): pii:ijms21113870.

Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs 20, 20 vs 27 and 27 vs 44 hours post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two similar clusters, showing overexpression at 20 relative to 8 hours and depletion at 27 and 44 hours, harboured the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the reversal of this trend during the hydrogenogenic phase.

RevDate: 2020-06-03

Du R, Wu Q, Y Xu (2020)

Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards.

Applied and environmental microbiology, 86(12): pii:AEM.00456-20.

Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies.IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.

RevDate: 2020-06-03
CmpDate: 2013-03-07

Lee HJ, Han SI, KS Whang (2012)

Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil.

International journal of systematic and evolutionary microbiology, 62(Pt 11):2589-2592.

A novel actinobacterium, designated strain BR-34(T), was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora. The strain contained iso-C(16 : 0) as the major fatty acid and MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34(T) formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908(T) (97.4% similarity), Catenulispora rubra Aac-30(T) (97.3%), Catenulispora yoronensis TT N02-20(T) (97.3%) and Catenulispora subtropica TT 99-48(T) (97%). However, the level of DNA-DNA relatedness between strain BR-34(T) and C. acidiphila ID139908(T) was only 45.32%. Based on DNA-DNA relatedness, morphological and phenotypic data, strain BR-34(T) could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora, for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34(T) (=KACC 15070(T)=NBRC 107755(T)).

RevDate: 2020-06-03
CmpDate: 2014-05-16

Lee HJ, Han SI, KS Whang (2012)

Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil.

International journal of systematic and evolutionary microbiology, 62(Pt 4):856-859.

Two actinobacterial strains, JR-43T and JR-4, were isolated from bamboo (Sasa borealis) rhizosphere soil. The isolates produced grey aerial mycelium and a yellow soluble pigment on ISP 4. Microscopic observation revealed that strains JR-43T and JR-4 produced rectiflexibiles spore chains with spiny surfaces. Both isolates had antibacterial activity against plant-pathogenic bacteria, such as Xanthomonas campestris LMG 568T and Xanthomonas axonopodis pv. vesicatoria LMG 905. The isolates contained iso-C14:0, iso-C15:0, anteiso-C15:0 and iso-C16:0 as the major fatty acids and MK-9(H6) and MK-9(H8) as the major isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences of strains JR-43T and JR-4 showed that they grouped within Streptomyces cluster II and had highest sequence similarity to Streptomyces seoulensis NBRC 16668T and Streptomyces recifensis NBRC 12813T (both 98.2 % 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain JR-43T and S. seoulensis NBRC 16668T and S. recifensis NBRC 12813T ranged from 31.42 to 42.92 %. Based on DNA-DNA relatedness and morphological and phenotypic data, strains JR-43T and JR-4 could be distinguished from the type strains of phylogenetically related species. They are therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces gramineus sp. nov. is proposed. The type strain is JR-43T (=KACC 15079T=NBRC 107863T). Strain JR-4 (=KACC 15078= NBRC 107864) is a reference strain [corrected].

RevDate: 2020-06-03
CmpDate: 2012-06-06

Han SI, Lee HJ, Lee HR, et al (2012)

Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis.

International journal of systematic and evolutionary microbiology, 62(Pt 3):632-637.

Three exopolysaccharide-producing bacteria, designated strains DRP28(T), DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8-97.4%. The major fatty acids were iso-C(15:0) and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28(T), DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9-42.7 mol% and DNA hybridization values of 82.6-86.8%; the strains exhibited DNA-DNA hybridization values of only 20.4-41.3% with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28(T), DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28(T) (=KACC 15075(T) =NBRC 107757(T)).

RevDate: 2020-06-03
CmpDate: 2012-04-30

Justé A, Van Trappen S, Verreth C, et al (2012)

Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.

International journal of systematic and evolutionary microbiology, 62(Pt 1):129-137.

Most bacteria recovered so far from sugar thick juice during storage represent strains of the species Tetragenococcus halophilus. Recently, several Gram-positive, non-motile, non-spore-forming cocci with other physiological and genetic traits were isolated from sugar thick juice samples from different origins. In this study, representative isolates were investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%. The level of DNA-DNA relatedness between isolate T1(T), representing the newly found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic features demonstrated that the isolates represent a novel species, for which the name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from high-salt and high-sugar environments showed clear differences in several physiological and genetic characteristics like RAPD fingerprints and 16S rRNA gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness between osmophilic and halophilic T. halophilus isolates, demonstrating that the different strains belong to the same species. Based on the phenotypic and genotypic differences observed, as well as the different origins of the strains and the industrial relevance of thick juice degradation, two subspecies of T. halophilus are described in this manuscript: T. halophilus subsp. halophilus subsp. nov. for the strains isolated from salt media and T. halophilus subsp. flandriensis subsp. nov. for the strains isolated from sugar-rich environments, which were first isolated in Flanders, Belgium. The type strains for the subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T) =DSM 23766(T)), respectively.

RevDate: 2020-06-02

van Bergeijk DA, Terlouw BR, Medema MH, et al (2020)

Ecology and genomics of Actinobacteria: new concepts for natural product discovery.

Nature reviews. Microbiology pii:10.1038/s41579-020-0379-y [Epub ahead of print].

Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.

RevDate: 2020-06-02

Roach TNF, Little M, Arts MGI, et al (2020)

A multiomic analysis of in situ coral-turf algal interactions.

Proceedings of the National Academy of Sciences of the United States of America pii:1915455117 [Epub ahead of print].

Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

RevDate: 2020-06-02

Costa OYA, de Hollander M, Pijl A, et al (2020)

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.

Microbiome, 8(1):76 pii:10.1186/s40168-020-00836-7.

BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.

RevDate: 2020-06-01

Bagnoud A, Pramateftaki P, Bogard MJ, et al (2020)

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.

Frontiers in microbiology, 11:771.

Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (Vmax), and CH4 concentration at half Vmax (KS) increased with CH4 supply. KS values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

RevDate: 2020-06-01

Zhang Z, van Kleunen M, Becks L, et al (2020)

Towards a General Understanding of Bacterial Interactions.

Trends in microbiology pii:S0966-842X(20)30136-0 [Epub ahead of print].

Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions.

RevDate: 2020-06-01

Sedighian N, Krijger M, Taparia T, et al (2020)

Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype IIB Sequevar 1) and Biovar 2T (Phylotype IIB Sequevar 25) Isolated from Lowlands in Iran.

Molecular plant-microbe interactions : MPMI [Epub ahead of print].

Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.

RevDate: 2020-05-31

Musonerimana S, Bez C, Licastro D, et al (2020)

Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot.

Microbial ecology pii:10.1007/s00248-020-01529-2 [Epub ahead of print].

Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.

RevDate: 2020-05-31

Liu RR, Tian Y, Zhou EM, et al (2020)

Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462T Improved Environmental Adaptability.

Microbial ecology pii:10.1007/s00248-020-01528-3 [Epub ahead of print].

Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.

RevDate: 2020-05-30

Su L, Zhang L, Nie D, et al (2020)

Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani.

Microorganisms, 8(6): pii:microorganisms8060806.

Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.

RevDate: 2020-05-29

Capson-Tojo G, Batstone DJ, Grassino M, et al (2020)

Purple phototrophic bacteria for resource recovery: Challenges and opportunities.

Biotechnology advances pii:S0734-9750(20)30064-1 [Epub ahead of print].

Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a "removal and disposal" approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g CODbiomass·g CODremoved-1)), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9, 0.3-2.2 and 0.1-0.3 $·kgdry biomass-1. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg-1) appears as a promising valorisation route.

RevDate: 2020-05-29

Rampal R, Wari N, Singh AK, et al (2020)

Retinoic Acid Is Elevated in the Mucosa of Patients With Active Ulcerative Colitis and Displays a Proinflammatory Role by Augmenting IL-17 and IFNγ Production.

Inflammatory bowel diseases pii:5848464 [Epub ahead of print].

BACKGROUND: All-trans retinoic acid (RA) plays a crucial role in promoting Foxp3+ Treg generation while reciprocally inhibiting Th1/Th17 generation. Our previous research highlighted that in the face of inflammatory conditions, RA plays a contrary role where it aggravates intestinal inflammation by promoting interferon (IFN) γ and interleukin (IL)-17 differentiation in vitro.

METHODS: In this study we translated our in vitro results into a clinical setting where we estimated mucosal and serum RA levels along with the immunophenotypic profile (IL-17, IFNγ, Foxp3, IL-10) in adaptive (CD4, CD8) and innate-like T cells (mucosal associated invariant T cells and γδ T cells) in patients with ulcerative colitis in remission or with active inflammation.

RESULTS: This is the first study to estimate RA levels in the human gut and shows that patients with active disease had increased mucosal RA levels as compared with patients in remission (4.0 vs 2.5 ng/mL; P < 0.01) and control patients (3.4 vs 0.8 ng/mL; P < 0.0001). This effect was accompanied by significantly elevated IL-17 and IFNγ in tissue CD4+, CD8+, mucosal associated invariant T+ cells, and γδ + T cells. Moreover, the raised RA levels in patients with active disease showed a positive correlation with proinflammatory cytokines (IL-17, IFNγ) and a negative correlation with IL-10. We also found that RA negatively correlated with IL-9, thereby reinstating our previous finding that RA inhibits Th9 differentiation.

CONCLUSIONS: These data confirm our previous in vitro results that in the presence of inflammation, RA plays a crucial role in maintaining gut inflammation by upregulating proinflammatory markers.

RevDate: 2020-05-29

Tschoeke D, Salazar VW, Vidal L, et al (2020)

Unlocking the Genomic Taxonomy of the Prochlorococcus Collective.

Microbial ecology pii:10.1007/s00248-020-01526-5 [Epub ahead of print].

Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.

RevDate: 2020-05-29

Van den Abbeele P, Ghyselinck J, Marzorati M, et al (2020)

In Vitro Evaluation of Prebiotic Properties of a Commercial Artichoke Inflorescence Extract Revealed Bifidogenic Effects.

Nutrients, 12(6): pii:nu12061552.

: Background: Prebiotics used as a dietary supplement, stimulate health-related gut microbiota (e.g., bifidobacteria, lactobacilli, etc.). This study evaluated potential prebiotic effects of an artichoke aqueous dry extract (AADE) using in vitro gut model based on the Simulator of Human Intestinal Microbial Ecosystem (SHIME®).

METHODS: Short-term colonic fermentations (48 h) of AADE, fructo-oligosaccharides (FOS), and a blank were performed. Microbial metabolites were assessed at 0, 6, 24, and 48 h of colonic incubation via measuring pH, gas pressure, lactate, ammonium, and short-chain fatty acids (SCFAs) levels. Community composition was assessed via targeted qPCRs.

RESULTS: After 24 and 48 h of incubation, bifidobacteria levels increased 25-fold with AADE (p < 0.05) and >100-fold with FOS (p < 0.05) compared to blank. Lactobacillus spp. levels only tended to increase with AADE, whereas they increased 10-fold with FOS. At 6 h, pH decreased with AADE and FOS and remained stable until 48 h; however, gas pressure increased significantly till the end of study. Acetate, propionate, and total SCFA production increased significantly with both at all time-points. Lactate levels initially increased but branched SCFA and ammonium levels remained low till 48 h.

CONCLUSION: AADE displayed prebiotic potential by exerting bifidogenic effects that stimulated production of health-related microbial metabolites, which is potentially due to inulin in AADE.

RevDate: 2020-05-29

Jia X, Dini-Andreote F, J Falcão Salles (2020)

Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data.

Microorganisms, 8(6): pii:microorganisms8060798.

Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that. RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities.

RevDate: 2020-05-28

Möhlmann TWR, Vogels CBF, Göertz GP, et al (2020)

Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes.

Microbial ecology pii:10.1007/s00248-020-01517-6 [Epub ahead of print].

Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.

RevDate: 2020-05-28

Yang M, Shi J, Wang B, et al (2020)

Control of Hydraulic Load on Bacterioplankton Diversity in Cascade Hydropower Reservoirs, Southwest China.

Microbial ecology pii:10.1007/s00248-020-01523-8 [Epub ahead of print].

Hydroelectric reservoirs are highly regulated ecosystems, where the understanding on bacterioplankton has been very limited so far. In view of significant changes in river hydrological conditions by dam construction, hydraulic load (i.e., the ratio of mean water depth to water retention time) was assumed to control bacterioplankton diversity in cascading hydropower reservoirs. To evaluate this hypothesis, we investigated bacterioplankton composition and diversity using high-throughput sequencing and related environmental variables in eleven reservoirs on the Wujiang River, Southwest China. Our results showed a decrease of bacterioplankton diversity index with an increase of reservoir hydraulic load. This is because hydraulic load governs dissolved oxygen variation in the water column, which is a key factor shaping bacterioplankton composition in these hydroelectric reservoirs. In contrast, bacterioplankton abundance was mainly affected by nutrient-related environmental factors. Therefore, from a hydrological perspective, hydraulic load is a decisive factor for the bacterioplankton diversity in the hydroelectric reservoirs. This study can improve the understanding of reservoir bacterial ecology, and the empirical relationship between hydraulic load and bacterioplankton diversity index will help to quantitatively evaluate ecological effects of river damming.

RevDate: 2020-05-28

Flanagan E, Lamport D, Brennan L, et al (2020)

Nutrition and the ageing brain: Moving towards clinical applications.

Ageing research reviews pii:S1568-1637(20)30214-2 [Epub ahead of print].

The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3rd Symposium on "Nutrition for the Ageing Brain: Moving Towards Clinical Applications" held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required.

RevDate: 2020-05-28

Roelofs D, Zwaenepoel A, Sistermans T, et al (2020)

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.

BMC biology, 18(1):57 pii:10.1186/s12915-020-00789-1.

BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals.

RESULTS: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs.

CONCLUSIONS: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.

RevDate: 2020-05-27

De Boeck I, van den Broek MFL, Allonsius CN, et al (2020)

Lactobacilli Have a Niche in the Human Nose.

Cell reports, 31(8):107674.

Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat.


ESP Quick Facts

ESP Origins

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
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Bellingham, WA 98226

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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).


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


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 )