A coexistence theory in microbial communities

Microbes are widespread in natural ecosystems where they create complex communities. Understanding the functions and dynamics of such microbial communities is a very important theme not only for ecology but also for humankind because microbes can play major roles in our health. Yet, it remains unclear how such complex ecosystems are maintained. Here, we present a simple theory on the dynamics of a microbial community. Bacteria preferring a particular pH in their environment indirectly inhibit the growth of the other types of bacteria by changing the pH to their optimum value. This pH-driven interaction always causes a state of bistability involving different types of bacteria that can be more or less abundant. Furthermore, a moderate abundance ratio of different types of bacteria can confer enhanced resilience to a specific equilibrium state, particularly when a trade-off relationship exists between growth and the ability of bacteria to change the pH of their environment. These results suggest that the balance of the composition of microbiota plays a critical role in maintaining microbial communities.

Download Full-text

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Microorganisms ◽

10.3390/microorganisms9040816 ◽

2021 ◽

Vol 9 (4) ◽

pp. 816

Author(s):

Matthew G. Links ◽

Tim J. Dumonceaux ◽

E. Luke McCarthy ◽

Sean M. Hemmingsen ◽

Edward Topp ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Dna Sequences ◽

Pcr Amplification ◽

Shotgun Sequencing ◽

Natural Ecosystems ◽

Gene Markers ◽

Microbial Profile ◽

Microbial Ecosystems ◽

Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Download Full-text

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples

10.1101/2020.09.17.302836 ◽

2020 ◽

Author(s):

Federica Pinto ◽

Moreno Zolfo ◽

Francesco Beghini ◽

Federica Armanini ◽

Francesco Asnicar ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Genetic Material ◽

Amplicon Sequencing ◽

Sample Type ◽

Natural Ecosystems ◽

Sediment Samples ◽

Water And Sediment ◽

Water And Sediment Samples

AbstractCultivation-free metagenomic analysis afforded unprecedented details on the diversity, structure and potential functions of microbial communities in different environments. When employed to study the viral fraction of the community that is recalcitrant to cultivation, metagenomics can shed light into the diversity of viruses and their role in natural ecosystems. However, despite the increasing interest in virome metagenomics, methodological issues still hinder the proper interpretation and comparison of results across studies. Virome enrichment experimental protocols are key multi-step processes needed for separating and concentrating the viral fraction from the whole microbial community prior to sequencing. However, there is little information on their efficiency and their potential biases. To fill this gap, we used metagenomic and amplicon sequencing to examine the microbial community composition through the serial filtration and concentration steps commonly used to produce viral-enriched metagenomes. The analyses were performed on water and sediment samples from an Alpine lake. We found that, although the diversity of the retained microbial communities declined progressively during the serial filtration, the final viral fraction contained a large proportion (from 10% to 40%) of non-viral taxa, and that the efficacy of filtration showed biases based on taxonomy. Our results quantified the amount of bacterial genetic material in viromes and highlighted the influence of sample type on the enrichment efficacy. Moreover, since viral-enriched samples contained a significant portion of microbial taxa, computational sequence analysis should account for such biases in the downstream interpretation pipeline.ImportanceFiltration is a commonly used method to enrich viral particles in environmental samples. However, there is little information on its efficiency and potential biases on the final result. Using a sequence-based analysis on water and sediment samples, we found that filtration efficacy is dependent on sample type and that the final virome contained a large proportion of non-viral taxa. Our finding stressed the importance of downstream analysis to avoid biased interpretation of data.

Download Full-text

Evaluation of texture in jelly gums incorporating berries and aromatic plants

Open Agriculture ◽

10.1515/opag-2020-0043 ◽

2020 ◽

Vol 5 (1) ◽

pp. 450-461

Author(s):

Raquel P. F. Guiné ◽

Paula M. R. Correia ◽

Cátia Reis ◽

Sofia G. Florença

Keyword(s):

Factor Analysis ◽

Critical Role ◽

Textural Properties ◽

The Other ◽

Strong Correlations ◽

Aromatic Plants ◽

Compression Properties ◽

Different Types ◽

Berry Fruits

AbstractIn the confectionery market, jelly gums are one of the most relevant sectors, being frequently consumed by many people, from children to adults. The present work intended to evaluate the textural properties in newly developed jelly gums made with berry fruits and herbs, given the critical role of texture in products with a gel-like structure. Four types of gums were developed (Strawberry & Anise, Strawberry & Mint, Raspberry & Mint, Blueberry & Mint) and their texture was evaluated through two types of tests (compression with a 75 mm probe and puncture with a 2 mm probe) allowing to calculate several textural properties. The results showed some differences between the two faces of the jelly gums analysed, i.e. on the top and on the bottom. As for the compression test, the Strawberry & Anise gums were among the softer (25.6 N) and with lower resilience (36.3%) and chewiness (16.9 N), despite being more adhesive (−0.5 N s). As for the puncture test, the sample Strawberry & Mint had the highest adhesiveness (−2.0 N s) but the lowest stickiness (−0.38 N). Additionally, very strong correlations were encountered between some of the properties studied (r = 0.861 or r = 0.822), and the factor analysis allowed defining three factors, the first clearly associated with the puncture properties while the other two were related to the compression properties. This work allowed concluding that the jelly gums presented different textural properties, particularly when assessed through different types of measurements. Hence, the use of different types of tests for texture analysis is recommended, since the results are complementary. This is relevant when developing food products intended for industrial production and commercialization.

Download Full-text

Composition and Physiological Profiling of Sprout-Associated Microbial Communities

Journal of Food Protection ◽

10.4315/0362-028x-65.12.1903 ◽

2002 ◽

Vol 65 (12) ◽

pp. 1903-1908 ◽

Cited By ~ 21

Author(s):

ANABELLE MATOS ◽

JAY L. GARLAND ◽

WILLIAM F. FETT

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

Carbon Sources ◽

The Other ◽

Independent Effect ◽

Patterns Of Utilization ◽

Plate Counts ◽

Alfalfa Sprouts

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30°C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 ± 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

Download Full-text

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

mSystems ◽

10.1128/msystems.00075-16 ◽

2016 ◽

Vol 1 (4) ◽

Cited By ~ 16

Author(s):

Mengxin Zhao ◽

Bo Sun ◽

Linwei Wu ◽

Qun Gao ◽

Feng Wang ◽

...

Keyword(s):

Microbial Community ◽

Microbial Biomass ◽

Microbial Communities ◽

Soil Type ◽

Critical Role ◽

Soil Types ◽

Functional Genes ◽

Soil Nitrification ◽

Microbial Responses

ABSTRACT Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available.

Download Full-text

Diversity of Microbial Communities under High Flocculating Characteristics by Biolog

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.316-317.618 ◽

2013 ◽

Vol 316-317 ◽

pp. 618-621

Author(s):

Shan Li ◽

Yan Bin Zhu ◽

Fang Ma ◽

Deng Xin Li

Keyword(s):

Microbial Community ◽

Activated Sludge ◽

Microbial Communities ◽

Functional Diversity ◽

The Other ◽

Diversity Analysis ◽

Pca Analysis ◽

Wastewater Samples ◽

High Level

So far, the study on diversity of microbial community which produces flocculating substances is relatively few. In this paper, soil, activated sludge and wastewater samples are collected from 21 different places, and then are cultivated in 5 different media. 5 different colony groups form large amounts of slime externally, which having high level of flocculation activities. Biolog is used to analysis the functional diversity of microbial communities.The microbial community BF-BCT having highest flocculating capability. The AWCD analysis results shows that the micro be in the BF-BCT utilized more carbons compared with the other six colony groups. In addition, the diversity analysis has similar conclusions with PCA analysis.

Download Full-text

Microbial contamination screening and interpretation for biological laboratory environments

10.1101/439570 ◽

2018 ◽

Author(s):

Xi Li ◽

Xue Zhu ◽

Wenjie Wang ◽

Kang Ning

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Indoor Environment ◽

Sampling Site ◽

Microbial Community Composition ◽

The Public ◽

Different Types ◽

Public Areas ◽

Microbial Contaminants ◽

Potential Impact

AbstractAdvances in microbiome researches have led us to the realization that the composition of microbial communities of indoor environment is profoundly affected by the function of buildings, and in turn may bring detrimental effects to the indoor environment and the occupants. Thus investigation is warranted for a deeper understanding of the potential impact of the indoor microbial communities. Among these environments, the biological laboratories stand out because they are relatively clean and yet are highly susceptible to microbial contaminants. In this study, we assessed the microbial compositions of samples from the surfaces of various sites across different types of biological laboratories. We have qualitatively and quantitatively assessed these possible microbial contaminants, and found distinct differences in their microbial community composition. We also found that the type of laboratories has a larger influence than the sampling site in shaping the microbial community, in terms of both structure and richness. On the other hand, the public areas of the different types of laboratories share very similar sets of microbes. Tracing the main sources of these microbes, we identified both environmental and human factors that are important factors in shaping the diversity and dynamics of these possible microbial contaminations in biological laboratories. These possible microbial contaminants that we have identified will be helpful for people who aim to eliminate them from samples.ImportanceMicrobial communities from biological laboratories might hamper the conduction of molecular biology experiments, yet these possible contaminations are not yet carefully investigated. In this work, a metagenomic approach has been applied to identify the possible microbial contaminants and their sources, from the surfaces of various sites across different types of biological laboratories. We have found distinct differences in their microbial community compositions. We have also identified the main sources of these microbes, as well as important factors in shaping the diversity and dynamics of these possible microbial contaminations. The identification and interpretation of these possible microbial contaminants in biological laboratories would be helpful for alleviate their potential detrimental effects.

Download Full-text

Microbial community-level features linked to divergent carbon flows during early litter decomposition in a constant environment

10.1101/659383 ◽

2019 ◽

Cited By ~ 3

Author(s):

Renee Johansen ◽

Michaeline Albright ◽

Deanna Lopez ◽

La Verne Gallegos-Graves ◽

Andreas Runde ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Litter Decomposition ◽

Plant Litter ◽

Carbon Flow ◽

Community Level ◽

Natural Ecosystems ◽

Long Term Storage ◽

Plant Litter Decomposition ◽

Underlying Mechanisms

AbstractDuring plant litter decomposition in soils, carbon has two general fates: return to the atmosphere via microbial respiration or transport into soil where long-term storage may occur. Discovering microbial community features that drive carbon fate from litter decomposition may improve modeling and management of soil carbon. This concept assumes there are features (or underlying processes) that are widespread among disparate communities, and therefore amenable to modeling. We tested this assumption using an epidemiological approach in which two contrasting patterns of carbon flow in laboratory microcosms were delineated as functional states and diverse microbial communities representing each state were compared to discover shared features linked to carbon fate. Microbial communities from 206 soil samples from the southwestern United States were inoculated on plant litter in microcosms, and carbon flow was measured as cumulative carbon dioxide (CO2) and dissolved organic carbon (DOC) after 44 days. Carbon flow varied widely among the microcosms, with a 2-fold range in cumulative CO2efflux and a 5-fold range in DOC quantity. Bacteria, not fungi, were the strongest drivers of DOC variation. The most significant community-level feature linked to DOC abundance was bacterial richness—the same feature linked to carbon fate in human-gut microbiome studies. This proof-of-principle study under controlled conditions suggests common features driving carbon flow in disparate microbial communities can be identified, motivating further exploration of underlying mechanisms that may influence carbon fate in natural ecosystems.

Download Full-text

CaptureSeq: Hybridization-based enrichment of cpn60 gene fragments reveals the community structures of synthetic and natural microbial ecosystems

10.1101/492116 ◽

2018 ◽

Author(s):

Matthew G. Links ◽

Tim J. Dumonceaux ◽

Luke McCarthy ◽

Sean M. Hemmingsen ◽

Edward Topp ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Shotgun Sequencing ◽

Natural Ecosystems ◽

Gene Markers ◽

Microbiome Composition ◽

Microbial Profile ◽

Domains Of Life ◽

Metagenome Sequencing ◽

Pcr Targeting

AbstractBackgroundMolecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics.MethodsWe present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir.ResultsThe CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health.

Download Full-text

Variation in Melitaea cinxia gut microbiota is phylogenetically highly structured but only mildly driven by host plant microbiota, sex or parasitism

10.1101/510446 ◽

2019 ◽

Cited By ~ 1

Author(s):

G. Minard ◽

G Tikhonov ◽

O. Ovaskainen ◽

M. Saastamoinen

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Host Plant ◽

Natural Populations ◽

Melitaea Cinxia ◽

Microbiota Composition ◽

Natural Ecosystems ◽

Phylogenetic Structure ◽

Plant Microbiota ◽

The Impact

Originality-Significance StatementThe factors contributing to the assembly of microbiota in animals are extremely complex, and thus a comprehensive understanding of the mechanisms shaping host-associated microbial communities in natural ecosystems requires extensive ecological studies and appropriate statistical methods. In this study, we investigated the bacterial microbiota associated with the caterpillars of the Glanville fritillary (Melitaea cinxia), which is a long-term-studied ecological model system. We assessed the structure of variation in both occurrence and abundance of gut microbial communities of individuals collected in the wild with joint-species modelling, with the aim to relate the microbial community structure with multiple potentially impacting covariates: host plant microbiota and metabolites, hosts’ sex, potential parasitoid infection, and family structure. These covariates exhibited substantial correlation with multiple microbial taxa’s occurrences, which correlations were consistent for phylogenetically related groups of taxa, but varied across the whole microbial community; on the contrary, only few correlations were found with taxa’s abundances. The dominating co-occurrence pattern of microbiota assembly, which effectively split caterpillar individuals into two distinct groups, was, however, unrelated to any of the considered covariates.SummaryUnderstanding of what ecological factors shape intraspecific variation of insect microbiota is still relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe the microbiome and to identify potential factors that determine the structure of the microbial community, including the sex of the host, the impact of parasitoid infection, and the possible link between host plant and caterpillar microbiota. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual. The observed variation in microbiota composition is partially attributed to the measured properties of the host or its plant microbial and chemical composition, and is aligned with microbial phylogenetic structure, with related taxa exhibiting similar patterns. However, the prevailing part of the observed variation was not associated with any of the assessed characteristics, although it followed a pronounced segregation structure: in some caterpillars the microbial communities were dominated by several related Enterobacteriaceae taxa, while in others these taxa were absent. Our results challenge previous findings that the host plant properties are the major drivers of microbiota communities of insect herbivores.

Download Full-text