Dataset Information

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

ABSTRACT: Symbiotic bacteria often help their hosts acquire nutrients from their diet, showing trends of co-evolution and independent acquisition by hosts from the same trophic levels. While these trends hint at important roles for biotic factors, the effects of the abiotic environment on symbiotic community composition remain comparably understudied. In this investigation, we examined the influence of abiotic and biotic factors on the gut bacterial communities of fish from different taxa, trophic levels and habitats. Phylogenetic and statistical analyses of 25 16S rRNA libraries revealed that salinity, trophic level and possibly host phylogeny shape the composition of fish gut bacteria. When analysed alongside bacterial communities from other environments, fish gut communities typically clustered with gut communities from mammals and insects. Similar consideration of individual phylotypes (vs. communities) revealed evolutionary ties between fish gut microbes and symbionts of animals, as many of the bacteria from the guts of herbivorous fish were closely related to those from mammals. Our results indicate that fish harbour more specialized gut communities than previously recognized. They also highlight a trend of convergent acquisition of similar bacterial communities by fish and mammals, raising the possibility that fish were the first to evolve symbioses resembling those found among extant gut fermenting mammals.

SUBMITTER: Sullam KE

PROVIDER: S-EPMC3882143 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

Sullam Karen E KE Essinger Steven D SD Lozupone Catherine A CA O'Connor Michael P MP Rosen Gail L GL Knight Rob R Kilham Susan S SS Russell Jacob A JA

Molecular ecology 20120404 13

Symbiotic bacteria often help their hosts acquire nutrients from their diet, showing trends of co-evolution and independent acquisition by hosts from the same trophic levels. While these trends hint at important roles for biotic factors, the effects of the abiotic environment on symbiotic community composition remain comparably understudied. In this investigation, we examined the influence of abiotic and biotic factors on the gut bacterial communities of fish from different taxa, trophic levels ...[more]

PMID: 22486918

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Project description:The giant panda has developed a series of evolutionary strategies to adapt to a bamboo diet. The abundance and diversity of the phyllosphere microbiome change dramatically depending on the season, host species, location, etc., which may, in turn, affect the growth and health of host plants. However, few studies have investigated the factors that influence phyllosphere bacteria in bamboo, a staple food source of the giant panda. Amplicon sequencing of the 16S rRNA gene was used to explore the abundance and diversity of phyllosphere bacteria in three bamboo species (Arundinaria spanostachya, Yushania lineolate, and Fargesia ferax) over different seasons (spring vs. autumn), elevation, distance from water, etc., in Liziping National Nature Reserve (Liziping NR), China. And whole-genome shotgun sequencing uncovered the differences in biological functions (KEGG and Carbohydrate-Active enzymes functions) of A. spanostachya phyllosphere bacteria between spring and autumn. The results showed that the abundance and diversity of F. ferax phyllosphere bacteria were greater than that of the other two bamboo species in both seasons. And three kinds of bamboo phyllosphere bacteria in autumn were significantly higher than in spring. The season was a more important factor than host bamboo species in determining the community structure of phyllosphere bacteria based on the (un)weighted UniFrac distance matrix. The composition, diversity, and community structure of phyllosphere bacteria in bamboo were primarily affected by the season, species, altitude, tree layer, and shrub layer. Different bacterial communities perform different functions in different bamboo species, and long-term low temperatures may shape more varied and complex KEGG and Carbohydrate-Active enzymes functions in spring. Our study presented a deeper understanding of factors influencing the bacterial community in the bamboo phyllosphere. These integrated results offer an original insight into bamboo, which can provide a reference for the restoration and management of giant panda bamboo food resources in the Xiaoxiangling mountains.

Project description:BackgroundExploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; however, the mechanism by which microorganisms specifically affect agricultural productivity is poorly understood. To clarify this uncertainly, the rhizospheric microbial communities of super rice plants at various growth stages were analysed using 16S rRNA high-throughput gene sequencing; microbial communities were then related to soil properties and rice productivity.ResultsThe rhizospheric bacterial communities were characterized by the phyla Proteobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia during all stages of rice growth. Rice production differed by approximately 30% between high- and low-yield sites that had uniform fertilization regimes and climatic conditions, suggesting the key role of microbial communities. Mantel tests showed a strong correlation between soil conditions and rhizospheric bacterial communities, and microorganisms had different effects on crop yield. Among the four growing periods, the rhizospheric bacterial communities present during the heading stage showed a more significant correlation (p < 0.05) with crop yield, suggesting their potential in regulating crop production. The biological properties (i.e., microbes) reflected the situation of agricultural land better than the physicochemical characterics (i.e., nutrient elements), which provides theoretical support for agronomic production. Molecular ecological network (MEN) analysis suggested that differences in productivity were caused by the interaction between the soil characteristics and the bacterial communities.ConclusionsDuring the heading stage of rice cropping, the rhizospheric microbial community is vital for the resulting rice yield. According to network analysis, the cooperative relationship (i.e., positive interaction) between between microbes may contribute significantly to yield, and the biological properties (i.e., microbes) better reflected the real conditions of agricultural land than did the physicochemical characteristics (i.e., nutrient elements).

Dataset Information

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

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Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

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