Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome

Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.

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Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass

Applied and Environmental Microbiology ◽

10.1128/aem.02795-14 ◽

2014 ◽

Vol 80 (23) ◽

pp. 7423-7432 ◽

Cited By ~ 20

Author(s):

Stephanie A. Eichorst ◽

Chijioke Joshua ◽

Noppadon Sathitsuksanoh ◽

Seema Singh ◽

Blake A. Simmons ◽

...

Keyword(s):

Microbial Communities ◽

Plant Biomass ◽

Biofuel Production ◽

Rrna Gene ◽

Gravimetric Analysis ◽

Content Type ◽

Biomass Deconstruction ◽

Bacterial Consortia ◽

Residual Biomass ◽

Chemical Pretreatments

ABSTRACTMicrobial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of theFirmicutes, theBacteroidetes, andDeinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.

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Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods

10.1101/2020.09.18.304485 ◽

2020 ◽

Author(s):

Gina R. Lewin ◽

Nicole M. Davis ◽

Bradon R. McDonald ◽

Adam J. Book ◽

Marc G. Chevrette ◽

...

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Species Interactions ◽

Plant Biomass ◽

Cellulose Degradation ◽

Soluble Sugars ◽

Mutual Exclusion ◽

Breakdown Product ◽

Rrna Gene ◽

Refuse Dumps

AbstractThe complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months), cellulolytic ability increased then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic and variably cellulolytic enrichment lines. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all the communities, with the mutual exclusion of specific cellulolytic taxa within individual enrichment lines and the high expression of genes associated with the production of antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities.ImportanceMicrobial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut.However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.

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Compositional data network analysis via lasso penalized D-trace loss

Bioinformatics ◽

10.1093/bioinformatics/btz098 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3404-3411 ◽

Cited By ~ 3

Author(s):

Huili Yuan ◽

Shun He ◽

Minghua Deng

Keyword(s):

Microbial Communities ◽

Compositional Data ◽

Sparse Matrix ◽

Mouse Skin ◽

Direct Interaction ◽

Interaction Network ◽

Gene Profiling ◽

Supplementary Information ◽

Rrna Gene ◽

Skin Microbiome

Abstract Motivation With the development of high-throughput sequencing techniques for 16S-rRNA gene profiling, the analysis of microbial communities is becoming more and more attractive and reliable. Inferring the direct interaction network among microbial communities helps in the identification of mechanisms underlying community structure. However, the analysis of compositional data remains challenging by the relative information conveyed by such data, as well as its high dimensionality. Results In this article, we first propose a novel loss function for compositional data called CD-trace based on D-trace loss. A sparse matrix estimator for the direct interaction network is defined as the minimizer of lasso penalized CD-trace loss under positive-definite constraint. An efficient alternating direction algorithm is developed for numerical computation. Simulation results show that CD-trace compares favorably to gCoda and that it is better than sparse inverse covariance estimation for ecological association inference (SPIEC-EASI) (hereinafter S-E) in network recovery with compositional data. Finally, we test CD-trace and compare it to the other methods noted above using mouse skin microbiome data. Availability and implementation The CD-trace is open source and freely available from https://github.com/coamo2/CD-trace under GNU LGPL v3. Supplementary information Supplementary data are available at Bioinformatics online.

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Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history

Biogeosciences ◽

10.5194/bg-14-4229-2017 ◽

2017 ◽

Vol 14 (18) ◽

pp. 4229-4241 ◽

Cited By ~ 14

Author(s):

Amy E. Goldman ◽

Emily B. Graham ◽

Alex R. Crump ◽

David W. Kennedy ◽

Elvira B. Romero ◽

...

Keyword(s):

Microbial Communities ◽

Reactive Transport ◽

Hyporheic Zone ◽

Microbial Respiration ◽

Co2 Flux ◽

Biogeochemical Cycling ◽

Microbial Interactions ◽

Rrna Gene ◽

Minor Effect ◽

Local Conditions

Abstract. The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet–dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic–terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at four elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose,  % C,  % N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

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Direct interaction network inference for compositional data via codaloss

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720020500377 ◽

2020 ◽

Vol 18 (06) ◽

pp. 2050037

Author(s):

Liang Chen ◽

Shun He ◽

Yuyao Zhai ◽

Minghua Deng

Keyword(s):

Microbial Communities ◽

Network Inference ◽

Compositional Data ◽

Direct Interaction ◽

Interaction Network ◽

16S Rrna Gene Sequencing ◽

Underlying Mechanism ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Microbiome Data

16S rRNA gene sequencing and whole microbiome sequencing make it possible and stable to quantitatively analyze the composition of microbial communities and the relationship among microbial communities, microbes, and hosts. One essential step in the analysis of microbiome compositional data is inferring the direct interaction network among microbial species, bringing to light the potential underlying mechanism that regulates interaction in their communities. However, standard statistical analysis may obtain spurious results due to compositional nature of microbiome data; therefore, network recovery of microbial communities remains challenging. Here, we propose a novel loss function called codaloss for direct microbes interaction network estimation under the sparsity assumptions. We develop an alternating direction optimization algorithm to obtain sparse solution of codaloss as estimator. Compared to other state-of-the-art methods, our model makes less assumptions about the microbial networks. The simulation and real microbiome data results show that our method outperforms other methods in network inference. An implementation of codaloss is available from https://github.com/xuebaliang/Codaloss .

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Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China

PeerJ ◽

10.7717/peerj.6044 ◽

2018 ◽

Vol 6 ◽

pp. e6044 ◽

Cited By ~ 2

Author(s):

Yan Zhu ◽

Yingying Cao ◽

Min Yang ◽

Pengchen Wen ◽

Lei Cao ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Different Origins ◽

Different Levels ◽

Different Origin

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

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Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis

Scientific Reports ◽

10.1038/s41598-020-74116-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Nighat Perveen ◽

Sabir Bin Muzaffar ◽

Ranjit Vijayan ◽

Mohammad Ali Al-Deeb

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Bacterial Communities ◽

Health Hazard ◽

Illumina Miseq ◽

Blood Feeding ◽

Microbial Interactions ◽

Rrna Gene ◽

Hyalomma Dromedarii

Abstract Hyalomma dromedarii is an important blood-feeding ectoparasite that affects the health of camels. We assessed the profile of bacterial communities associated with H. dromedarii collected from camels in the eastern part of the UAE in 2010 and 2019. A total of 100 partially engorged female ticks were taken from tick samples collected from camels (n = 100; 50/year) and subjected to DNA extraction and sequencing. The 16S rRNA gene was amplified from genomic DNA and sequenced using Illumina MiSeq platform to elucidate the bacterial communities. Principle Coordinates Analysis (PCoA) was conducted to determine patterns of diversity in bacterial communities. In 2010 and 2019, we obtained 899,574 and 781,452 read counts and these formed 371 and 191 operational taxonomic units (OTUs, clustered at 97% similarity), respectively. In both years, twenty-five bacterial families with high relative abundance were detected and the following were the most common: Moraxellaceae, Enterobacteriaceae, Staphylococcaceae, Bacillaceae, Corynebacteriaceae, Flavobacteriaceae, Francisellaceae, Muribaculaceae, Neisseriaceae, and Pseudomonadaceae. Francisellaceae and Enterobacteriaceae coexist in H. dromedarii and we suggest that they thrive under similar conditions and microbial interactions inside the host. Comparisons of diversity indicated that microbial communities differed in terms of richness and evenness between 2010 and 2019, with higher richness but lower evenness in communities in 2010. Principle coordinates analyses showed clear clusters separating microbial communities in 2010 and 2019. The differences in communities suggested that the repertoire of microbial communities have shifted. In particular, the significant increase in dominance of Francisella and the presence of bacterial families containing pathogenic genera shows that H. dromedarii poses a serious health risk to camels and people who interact with them. Thus, it may be wise to introduce active surveillance of key genera that constitute a health hazard in the livestock industry to protect livestock and people.

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Carbon cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history

10.5194/bg-2017-28 ◽

2017 ◽

Cited By ~ 1

Author(s):

Amy E. Goldman ◽

Emily B. Graham ◽

Alex R. Crump ◽

David W. Kennedy ◽

Elvira B. Romero ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Cycling ◽

Reactive Transport ◽

Hyporheic Zone ◽

Microbial Respiration ◽

Co2 Flux ◽

Microbial Interactions ◽

Rrna Gene ◽

Minor Effect ◽

Local Conditions

Abstract. The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet/dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding carbon cycling at the aquatic–terrestrial interface and to creating robust hydrobiogeochemical models. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated reinundation. Surface sediment for assays and forced inundation laboratory incubations (destructively sampled at 0.5 hours and 25 hours) was collected at four elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sampling elevations were inundated by the river 0 days, 13 days, 127 days, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, % C, % N) and microbial communities (16S and ITS rRNA gene sequencing, qPCR) were driven by differences in elevation and thus inundation history. Microbial respiration did not differ significantly across elevations prior to inundation. Inundation suppressed microbial respiration relative to uninundated sediment across all elevations, but the degree of suppression was dramatically different between the elevations saturated and unsaturated during sampling, indicating a binary threshold response. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO2. Upon re–wetting, microbial communities are initially suppressed metabolically, which results in lower CO2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts via a shift in composition. Our results indicate that the time between inundation events can push the system into alternate states: we suggest that (i) above some threshold of inundation–interval, re–inundation suppresses respiration to a consistent, low rate, and (ii) that below some inundation–interval, re–inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

2020 ◽

Vol 48 (2) ◽

pp. 399-409

Author(s):

Baizhen Gao ◽

Rushant Sabnis ◽

Tommaso Costantini ◽

Robert Jinkerson ◽

Qing Sun

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Environmental Remediation ◽

Real Life ◽

Design Principles ◽

Microbial Interactions ◽

Potential Applications ◽

New Gene ◽

Global Biogeochemical Cycles ◽

Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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