scholarly journals A probabilistic model to identify the core microbial community

2018 ◽  
Author(s):  
Thiago Gumiere ◽  
Kyle M. Meyer ◽  
Adam R. Burns ◽  
Silvio J. Gumiere ◽  
Brendan J. M. Bohannan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Probabilistic Model ◽  
Plant Disease ◽  
Probabilistic Method ◽  
Community Studies ◽  
Community Based ◽  
The Core ◽  
Probable Occurrence

ABSTRACTThe core microbial community has been hypothesized to have essential functions ranging from maintaining health in animals to protection against plant disease. However, the identification of the core microbial community is frequently based on arbitrary thresholds, selecting only the most abundant microorganisms. Here, we developed and tested an approach to identify the core community based on a probabilistic model. The Poisson distribution was used to identify OTUs with a probable occurrence in every sample of a given dataset. We identified the core communities of four extensive microbial datasets, and compared the results with conventional, but arbitrary, methods. The datasets were composed of the microbiomes of humans (tongue, gut, and skin), mice (gut), plant (grapevine) tissue, and the maize rhizosphere. Our proposed method revealed core microbial communities with higher richness and diversity than those previously described. This method also includes a greater number of rare taxa in the core, which are often neglected by arbitrary threshold methods. We demonstrated that our proposed method revels a probable core microbial community for each different habitat, which extend our knowledge about shared microbial communities. Our proposed method may help the next steps proving the essential functions of core microbial communities.Originality-Signifìcance StatementMore rigorous and less arbitrary statistical methods could increase knowledge regarding the role of microorganisms and their interactions. Here, we suggest a probabilistic method to identify the microbial core community across systems. Our method identifies a large proportion of the rare community that likely belongs to the microbial core community, which was not identified by conventional methods. Our probabilistic model is a non-arbitrary approach to defining the microbial core community, which may help in the next step of the microbial core community studies.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

scholarly journals Microbial community structure in the western tropical South Pacific

2018 ◽  
Vol 15 (12) ◽  
pp. 3909-3925 ◽  
Author(s):  
Nicholas Bock ◽  
France Van Wambeke ◽  
Moïra Dion ◽  
Solange Duhamel
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
N2 Fixation ◽  
Phytoplankton Biomass ◽  
South Pacific ◽  
Global Ocean ◽  
Bottom Up

Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

The James and Grace Lee Boggs School

2017 ◽  
Author(s):  
Julia Putnam ◽  
Amanda Rosman ◽  
Marisol Teachworth
Keyword(s):  
Charter School ◽  
Natural World ◽  
Core Values ◽  
Community Empowerment ◽  
Community Members ◽  
Community Based ◽  
Human Relationships ◽  
Critical Thought ◽  
The Core

The James and Grace Lee Boggs School is a community-based public charter school on the east side of Detroit. It employs a placed-based model of learning, which is rooted in the local. This means that it stems from history, geography, community members, businesses, and the challenges and possibilities in the community. The core values of the school are: high levels of critical thought; creativity and learning; excellence in teaching; authentic and trusting relationships; community empowerment; and equity within both human relationships and the natural world. The core purpose is: to provide the tools to achieve ambitious goals and live lives of meaning, to nurture a sense of place and develop a commitment to a better Detroit, and to grow our souls by developing a connection with ourselves, each other, and the earth. This interview chapter is with Julia Putnam, Amanda Rosman, and Marisol Teachworth: the three co-founders of the school. They were influenced by the philosophies of Grace and Jimmy Boggs and the school was born out of many conversations about the role of education in a city like Detroit.

scholarly journals Emergence Shapes the Structure of the Seed Microbiota

2014 ◽  
Vol 81 (4) ◽  
pp. 1257-1266 ◽  
Author(s):  
Matthieu Barret ◽  
Martial Briand ◽  
Sophie Bonneau ◽  
Anne Préveaux ◽  
Sophie Valière ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Practical Applications ◽  
Bacterial Marker ◽  
Species Specific ◽  
Diversity Studies

ABSTRACTSeeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment ofgyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Interspecific social interactions shape public goods production in natural microbial communities

2019 ◽  
Author(s):  
Elze Hesse ◽  
Siobhan O’Brien ◽  
Adela M. Luján ◽  
Florian Bayer ◽  
Eleanor M. van Veen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Public Goods ◽  
Social Interactions ◽  
Microbial Communities ◽  
Interspecific Interactions ◽  
Similar Time ◽  
Focal Species ◽  
Ecological Selection ◽  
Social Behaviours

AbstractSome microbial public goods benefit conspecifics, as well as other species. Here, we use evolution and competition experiments to determine how exploitation of public goods by the wider microbial community shapes the production of an interspecific public good: metal-detoxifying siderophores. By simultaneously studying whole microbial communities and an embedded focal species, we show that interspecific exploitation results in both ecological selection against microbial taxa that produce relatively large amounts of siderophores, and evolution of reduced siderophore production within taxa over similar time scales. Our findings demonstrate the crucial role of interspecific interactions in shaping microbial social behaviours.One sentence summary –Interspecific exploitation shapes the evolution and ecology of public goods production

scholarly journals Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Alejandra Hernández-Terán ◽  
Marcelo Navarro-Díaz ◽  
Mariana Benítez ◽  
Rafael Lira ◽  
Ana Wegier ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Community Diversity ◽  
Rrna Gene ◽  
Host Genotype ◽  
Plant Host ◽  
Wild Cotton

ABSTRACT The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.

scholarly journals Microbiome of Grand Canyon Caverns, a dry sulfuric karst cave in Arizona, supports diverse extremo-philic bacterial and archaeal communities

2021 ◽  
Vol 83 (1) ◽  
pp. 44-56
Author(s):  
Raymond Keeler ◽  
Bradley Lusk
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Grand Canyon ◽  
Rrna Gene ◽  
Karst Cave ◽  
Operational Taxonomic Units ◽  
Karst Caves ◽  
Bacterial And Archaeal Communities ◽  
Karst Systems

We analyzed the microbial community of multicolored speleosol deposits found in Grand Canyon Caverns, a dry sulfuric karst cave in northwest Arizona, USA. Underground cave and karst systems harbor a great range of microbial diversity; however, the inhabitants of dry sulfuric karst caves, including extremophiles, remain poorly understood. Understanding the microbial communities inhabiting cave and karst systems is essential to provide information on the multidirectional feedback between biology and geology, to elucidate the role of microbial biogeochemical processes on cave formation, and potentially aid in the development of biotechnology and pharmaceuticals. Based on the V4 region of the 16S rRNA gene, the microbial community was determined to consist of 2207 operational taxonomic units (OTUs) using species-level annotations, representing 55 phyla. The five most abundant Bacteria were Actinobacteria 51.3 ± 35.4 %, Proteobacteria 12.6 ± 9.5 %, Firmicutes 9.8 ± 7.3 %, Bacteroidetes 8.3 ± 5.9 %, and Cyanobacteria 7.1 ± 7.3 %. The relative abundance of Archaea represented 1.1 ± 0.9 % of all samples and 0.2 ± 0.04 % of samples were unassigned. Elemental analysis found that the composition of the rock varied by sample and that calcium (6200 ± 3494 ppm), iron (1141 ± 1066 ppm), magnesium (25 ± 17 ppm), and phosphorous (37 ± 33 ppm) were the most prevalent elements detected across all samples. Furthermore, carbon, hydrogen, and nitrogen were found to compose 4.7 ± 4.9 %, 0.3 ± 0.4 %, and 0.1 ± 0.1 % of samples, respectively. Finally, Raman spectra compared to the RRUFF Project database using CrystalSleuth found that the mineral composition of the speleosol consisted of calcite, hematite, paraspurrite, quartz, and trattnerite. These data suggest that dry sulfuric karst caves can harbor robust microbial communities under oligotrophic, endolithic, and troglophilic conditions.

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