Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

ABSTRACTSerpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

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Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

Applied and Environmental Microbiology ◽

10.1128/aem.00527-11 ◽

2011 ◽

Vol 77 (21) ◽

pp. 7560-7567 ◽

Cited By ~ 17

Author(s):

Marketa Sagova-Mareckova ◽

Marek Omelka ◽

Ladislav Cermak ◽

Zdenek Kamenik ◽

Jana Olsovska ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Ph ◽

Soil Chemistry ◽

High Performance ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Carbon Sources ◽

Soil Extracts

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

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Application of Methods for Identifying Broiler Chicken Gut Bacterial Species Linked with Increased Energy Metabolism

Applied and Environmental Microbiology ◽

10.1128/aem.01384-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 783-791 ◽

Cited By ~ 105

Author(s):

Valeria A. Torok ◽

Kathy Ophel-Keller ◽

Maylene Loo ◽

Robert J. Hughes

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Metabolizable Energy ◽

Principal Coordinates ◽

Improved Performance ◽

Gut Microbial Community

ABSTRACT A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

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Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

10.1101/2020.10.09.333336 ◽

2020 ◽

Cited By ~ 1

Author(s):

Samir Giri ◽

Leonardo Oña ◽

Silvio Waschina ◽

Shraddha Shitut ◽

Ghada Yousif ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Bacterial Species ◽

Exchange Interactions ◽

Structure And Function ◽

Phylogenetic Distance ◽

And Function ◽

Microbial Community Assembly ◽

Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

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Plant species and soil type influence rhizosphere bacterial composition and seedling establishment on serpentine soils

10.1101/489344 ◽

2018 ◽

Cited By ~ 1

Author(s):

Alexandria N. Igwe ◽

Rachel L. Vannette

Keyword(s):

Microbial Community ◽

Plant Growth ◽

Microbial Communities ◽

Plant Species ◽

Soil Chemistry ◽

Seedling Survival ◽

Serpentine Soils ◽

Bacterial Composition ◽

Plant Phenotype ◽

Community Source

AbstractRoot-associated microbial communities influence plant phenotype, growth and local abundance, yet the factors that structure these microbial communities are still poorly understood. California landscapes contain serpentine soils, which are nutrient-poor and high in heavy metals, and distinct from neighboring soils. Here, we surveyed the rhizoplane of serpentine-indifferent plants species growing on serpentine and non-serpentine soils to determine the relative influence of plant identity and soil chemistry on rhizoplane microbial community structure using 16S rRNA metabarcoding. Additionally, we experimentally examined if locally adapted microorganisms enhance plant growth in serpentine soil. Plant species, soil chemistry, and the interaction between them were important in structuring rhizoplane bacterial communities in both the field and experimental soils. In the experiment, rhizoplane microbial community source influenced seedling survival, but plant growth phenotypes measured were largely invariant to microbial community with a few exceptions. Results from the field sampling suggest that plant species associate with specific microbial communities even across chemically distinct soils, and that microbial communities can differentially influence seedling survival on harsh serpentine soils.

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Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes

10.1101/259861 ◽

2018 ◽

Cited By ~ 5

Author(s):

Thea Van Rossum ◽

Miguel I. Uyaguari-Diaz ◽

Marli Vlok ◽

Michael A. Peabody ◽

Alvin Tian ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Single Site ◽

Microbial Dynamics ◽

Microbial Composition ◽

Time Space ◽

Chemical Conditions ◽

Over Time

AbstractFreshwater is an essential resource of increasing value, as clean water sources diminish. Microorganisms in rivers, a major source of renewable freshwater, are significant due to their role in drinking water safety, signalling environmental contamination1, and driving global nutrient cycles2,3. However, a foundational understanding of microbial communities in rivers is lacking4, especially temporally and for viruses5‒7. No studies to date have examined the composition of the free-floating river virome over time, and explanations of the underlying causes of spatial and temporal changes in riverine microbial composition, especially for viruses, remain unexplored. Here, we report relationships among riverine microbial communities and their environment across time, space, and superkingdoms (viruses, bacteria, and microeukaryotes), using metagenomics and marker-based microbiome analysis methods. We found that many superkingdom pairs were synchronous and had consistent shifts with sudden environmental change. However, synchrony strength, and relationships with environmental conditions, varied across space and superkingdoms. Variable relationships were observed with seasonal indicators and chemical conditions previously found to be predictive of bacterial community composition4,8‒10, emphasizing the complexity of riverine ecosystems and raising questions around the generalisability of single-site and bacteria-only studies. In this first study of riverine viromes over time, DNA viral communities were stably distinct between sites, suggesting the similarity in riverine bacteria across significant geographic distances10‒12does not extend to viruses, and synchrony was surprisingly observed between DNA and RNA viromes. This work provides foundational data for riverine microbial dynamics in the context of environmental and chemical conditions and illustrates how a bacteria-only or single-site approach would lead to an incorrect description of microbial dynamics. We show how more holistic microbial community analysis, including viruses, is necessary to gain a more accurate and deeper understanding of microbial community dynamics.

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Maize (Zea Mays L.) Genotypes Induce the Changes of Rhizosphere Microbial Communities

10.21203/rs.3.rs-1183026/v1 ◽

2021 ◽

Author(s):

Yuehan Li ◽

Zheng Qu ◽

Weihui Xu ◽

Wenjing Chen ◽

Yunlong Hu ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

High Throughput Sequencing ◽

Zea Mays L ◽

Bioinformatics Analysis ◽

Bacterial Community Composition ◽

Maize Genotypes ◽

Microbe Interactions ◽

And Function ◽

Rhizosphere Microbial Community

Abstract Plant-microbe interactions affect ecosystem function, and plant species influence relevant microorganisms. However, the different genotypes of maize that shape the structure and function of the rhizosphere microbial community remain poorly investigated. During this study, the structures of the rhizosphere microbial community among three genotypes of maize were analyzed at the seedling and maturity stages using high-throughput sequencing and bioinformatics analysis. The results demonstrated that Tiannuozao 60 (N) showed higher bacterial and fungal diversity in both periods, while Junlong1217 (QZ) and Fujitai519 (ZL) had lower diversity. The bacterial community structure among the three varieties was significantly different; however, fewer differences were found in the fungal community. The bacterial community composition of N and QZ was similar yet different from ZL at the seedling stage. The bacterial networks of the three cultivars were more complex than the fungal networks, and the networks of the mature stages were more complex than those of the seedling stages, while the opposite was true for the fungi. FAPROTAX functional and FUNGuild functional predictions revealed that different varieties of maize were different in functional abundance at the genus level, and these differences were related to breeding characteristics. This study suggested that different maize genotypes regulated the rhizosphere bacterial and fungal communities, which would help guide practices.

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

10.1101/736843 ◽

2019 ◽

Cited By ~ 2

Author(s):

Diana J. Rennison ◽

Seth M. Rudman ◽

Dolph Schluter

Keyword(s):

Microbial Communities ◽

Local Adaptation ◽

Biotic Interactions ◽

Ecological Speciation ◽

Microbiome Composition ◽

Interacting Species ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

And Function ◽

Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

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Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

10.1101/2020.12.12.420737 ◽

2020 ◽

Author(s):

Saeed Keshani Langroodi ◽

Yemin Lan ◽

Ben Stenuit ◽

Gail Rosen ◽

Joseph B Hughes ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Metagenomic Data ◽

Military Conflict ◽

Nitro Explosives ◽

And Function ◽

Aerobic And Anaerobic

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented.

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Inferring directional relationships in microbial communities using signed Bayesian networks

BMC Genomics ◽

10.1186/s12864-020-07065-0 ◽

2020 ◽

Vol 21 (S6) ◽

Author(s):

Musfiqur Sazal ◽

Kalai Mathee ◽

Daniel Ruiz-Perez ◽

Trevor Cickovski ◽

Giri Narasimhan

Keyword(s):

Microbial Community ◽

Bayesian Networks ◽

Bayesian Network ◽

Microbial Communities ◽

Community Analysis ◽

Vital Role ◽

Microbe Interactions ◽

Health And Disease ◽

Colonization Patterns ◽

Host Microbe Interactions

Abstract Background Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations. Results In this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian Network (sBN). We report a surprising association between directed edges in signed BNs and known colonization orders. Conclusions BNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.

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