scholarly journals Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

2019 ◽  
Vol 1 (1) ◽  
pp. 112-128 ◽  
Author(s):  
Jiwen Liu ◽  
Zhe Meng ◽  
Xiaoyue Liu ◽  
Xiao-Hua Zhang
Keyword(s):  
Microbial Community ◽  
Ecosystem Functioning ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Compositional Data ◽  
Marker Gene ◽  
Microbial Community Composition ◽  
Gene Transcription Level ◽  
Occurrence Patterns ◽  
Phylogenetic Divergence

Abstract Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Through correlation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receiving increasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibits significant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community, but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of community members. Furthermore, the huge amount of microbial community data has significantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findings in microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of different aspects, derived from community compositional data.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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

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.

scholarly journals Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Janneke Schreuder ◽  
Francisca C. Velkers ◽  
Alex Bossers ◽  
Ruth J. Bouwstra ◽  
Willem F. de Boer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Intestinal Microbiota ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Sudden Change ◽  
Rrna Gene ◽  
Poultry House ◽  
Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

scholarly journals Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Gemma Henderson ◽  
◽  
Faith Cox ◽  
Siva Ganesh ◽  
Arjan Jonker ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Methanogenic Archaea ◽  
Methane Formation ◽  
Core Microbiome ◽  
Rumen Microbes ◽  
Metabolic Interactions ◽  
Occurrence Patterns ◽  
Dominant Bacteria

Abstract Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

scholarly journals Microbial community composition in Brazilian stored diesel fuel of varying sulfur content, using high-throughput sequencing

Fuel ◽  
2017 ◽  
Vol 189 ◽  
pp. 340-349 ◽  
Author(s):  
Aline Oliboni de Azambuja ◽  
Francielle Bücker ◽  
Patrícia Dörr de Quadros ◽  
Kateryna Zhalnina ◽  
Raquel Dias ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Sulfur Content ◽  
High Throughput ◽  
Diesel Fuel ◽  
High Throughput Sequencing ◽  
Microbial Community Composition

scholarly journals Response of Soil Microbial Community Structure and Function to Different Altitudes in Arid Valley in Panzhihua, China

2021 ◽  
Author(s):  
Runji Zhang ◽  
Xianrui Tian ◽  
Quanju Xiang ◽  
Petri Penttinen ◽  
Yunfu Gu
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Environmental Changes ◽  
Microbial Community Composition ◽  
Chemical Properties ◽  
Microbial Biomass C ◽  
Chemical Characteristics ◽  
Soil Microbial Community Structure ◽  
Available N ◽  
Different Altitudes

Abstract Background: Altitude affects biodiversity and physic-chemical properties of soil, providing natural sites for studying species distribution and the response of biota to environmental changes. We sampled soil at three altitudes in an arid valley, determined the physic-chemical characteristics and microbial community composition in the soils, identified differentially abundant taxa and the relationships between community composition and environmental factors. Results: The low, medium and high altitudes were roughly separated based on the physic-chemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in all measured factors except pH. The contents of organic and microbial biomass C, total and available N and available P, and the richness and diversity of the microbial communities were lowest in the medium altitude. The relative abundances of phyla Proteobacteria, Gemmatimonadetes, Actinobacteria and Acidobacteria were high at all altitudes. The differentially abundant ASVs were mostly assigned to Proteobacteria and Acidobacteria. The highest number of ASVs characterizing altitude were detected in the high altitude. However, the predicted functions of the communities were overlapping, suggesting that the contribution of the communities to soil processes changed relatively little along the altitude gradient. Conclusions: The composition of microbial community at different altitudes was related to the differences of all measuring factors except pH in arid valley in Panzhihua, China.

scholarly journals Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

2021 ◽  
Author(s):  
Laís Farias Oliveira Lima ◽  
Amanda Alker ◽  
Bhavya Papudeshi ◽  
Megan Morris ◽  
Robert Edwards ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nutrient Cycling ◽  
Ecosystem Functioning ◽  
Environmental Changes ◽  
Coral Host ◽  
Shotgun Metagenomics ◽  
Patch Reefs ◽  
Coral Microbiome ◽  
Gene Functions ◽  
Coral Health

Abstract Background The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes and tied to ecosystem functioning, as it constitutes the direct interface between the coral host and the environment. The functional profile of microbial genes in the coral SML is underexplored and the use of shotgun metagenomics is relatively rare among coral microbiome studies. Here we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. Results The analysis was conducted using metagenomes and metagenome assemble genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs . Our results showed that the microbial community structure is simultaneously selected by the host medium (i.e., coral SML versus water) and the local environment (i.e., inner reefs versus outer reefs), both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and that are related to higher levels of microbial activity, competition, and stress response, such as dimethylsulfoniopropionate (DMSP) breakdown. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. Conclusion The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome; potentially increasing holobiont resilience to environmental changes and disease. Our results reveal microbial taxa and functions selected at reef scale in the coral SML microbiome that can leverage disease management, microbiome engineering, and microbial eco-evolutionary theories.

Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms

2019 ◽  
Vol 95 (6) ◽  
Author(s):  
Anders Bjørnsgaard Aas ◽  
Carrie J Andrew ◽  
Rakel Blaalid ◽  
Unni Vik ◽  
Håvard Kauserud ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Structure ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Diversity Patterns ◽  
Bistorta Vivipara ◽  
Adjacent Soil ◽  
Bacteria And Fungi

ABSTRACT The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

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