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Microbiome facing disturbance: common response of the rare biosphere from the three domains of life

ABSTRACT: Microbiome facing disturbance: common response of the rare biosphere from the three domains of life

PROVIDER: PRJEB46483 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6336670_1.fastq.gz	Fastqsanger.gz
	ERR6336670_2.fastq.gz	Fastqsanger.gz
	ERR6336680_1.fastq.gz	Fastqsanger.gz
	ERR6336680_2.fastq.gz	Fastqsanger.gz
	ERR6336671_1.fastq.gz	Fastqsanger.gz

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Microbiome facing disturbance: common response of the rare biosphere from the three domains of life

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Project description:A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

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Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.

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