Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

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Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽

10.1128/mbio.01851-20 ◽

2020 ◽

Vol 11 (4) ◽

Author(s):

Andrew Oliver ◽

Brandon LaMere ◽

Claudia Weihe ◽

Stephen Wandro ◽

Karen L. Lindsay ◽

...

Keyword(s):

Mass Spectrometry ◽

Reproductive Health ◽

Microbial Communities ◽

Carbon Sources ◽

Amplicon Sequencing ◽

Vaginal Microbiome ◽

Content Type ◽

Healthy Women ◽

Healthy Pregnancy ◽

Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

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The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa056 ◽

2020 ◽

Vol 96 (6) ◽

Cited By ~ 3

Author(s):

A Katsoula ◽

S Vasileiadis ◽

M Sapountzi ◽

Dimitrios G Karpouzas

Keyword(s):

Microbial Communities ◽

Agricultural Production ◽

Soil Microorganisms ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Similar Response ◽

Repeated Application ◽

Plant Leaves ◽

Soil System ◽

Plant Soil

ABSTRACT Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant–soil system and agricultural production.

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Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa042 ◽

2020 ◽

Vol 2 (2) ◽

Author(s):

Pengshuo Yang ◽

Chongyang Tan ◽

Maozhen Han ◽

Lin Cheng ◽

Xuefeng Cui ◽

...

Keyword(s):

Microbial Communities ◽

Large Scale ◽

Network Connectivity ◽

Small Range ◽

Environmental Disturbance ◽

Target Species ◽

Important Species ◽

Metagenome Analysis ◽

Occurrence Patterns ◽

Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

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A network-based approach to deciphering a dynamic microbiome’s response to a subtle perturbation

Scientific Reports ◽

10.1038/s41598-020-73920-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Grace Tzun-Wen Shaw ◽

An-Chi Liu ◽

Chieh-Yin Weng ◽

Yi-Chun Chen ◽

Cheng-Yu Chen ◽

...

Keyword(s):

Microbial Communities ◽

Ecosystem Functioning ◽

Environmental Changes ◽

Ecosystem Dynamics ◽

Environmental Research ◽

Human Society ◽

The Past ◽

Environmental Perturbations ◽

Before And After ◽

Occurrence Patterns

Abstract Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

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The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

Biogeosciences Discussions ◽

10.5194/bgd-12-18103-2015 ◽

2015 ◽

Vol 12 (21) ◽

pp. 18103-18150 ◽

Cited By ~ 3

Author(s):

L. Purkamo ◽

M. Bomberg ◽

R. Kietäväinen ◽

H. Salavirta ◽

M. Nyyssönen ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Fixation ◽

Keystone Species ◽

Carbon Assimilation ◽

Sugar Metabolism ◽

Archaeal Community ◽

Amino Sugar ◽

Amplicon Sequencing ◽

Fracture Zones ◽

Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

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High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

10.21203/rs.3.rs-34433/v1 ◽

2020 ◽

Author(s):

Wu Qu ◽

Boliang Gao ◽

Jie Wu ◽

Min Jin ◽

Jianxin Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Fungal Community ◽

Amplicon Sequencing ◽

Biotic Factors ◽

Community Structures ◽

Mangrove Sediments ◽

Element Cycling ◽

Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charles S. Cockell ◽

Bettina Schaefer ◽

Cornelia Wuchter ◽

Marco J. L. Coolen ◽

Kliti Grice ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Granitic Rocks ◽

Rrna Gene ◽

Deep Biosphere ◽

Deep Subsurface ◽

Cell Biomass ◽

Colonization Potential ◽

The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

10.1101/197855 ◽

2017 ◽

Author(s):

Eric R Hester ◽

Sarah F. Harpenslager ◽

Josepha MH van Diggelen ◽

Leon L Lamers ◽

Mike SM Jetten ◽

...

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Amplicon Sequencing ◽

N Fertilization ◽

Wetland Soil ◽

N Availability ◽

Gas Emissions ◽

16S Rrna Amplicon Sequencing ◽

N Input

AbstractWetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere ofJuncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations withJ. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

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