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Tracking carbon-flow from naphthalene degrading bacteria in coal-tar contaminated surface sediments and groundwater.

ABSTRACT: In the first part of the experiment, naphthalene contaminated surface sediments, where effluent from the coal-tar contaminated groundwater surfaces, were incubated in situ with either 13C-labeled or natural abundance 13C-naphthalene at various dosing regimes. The dosing regimes correspond with 3 doses in a 24 hr timespan 5 doses in a 72 hr timespan and 8 doses in 8 days. Shotgun metagenome libraries were prepared in triplicate from all 13C-labeled sediments following the enrichment for 13C-labeled DNA. Sediments fed natural abundance 12C-naphthalene were not replicated, but where exposed to the identical handling as DNA extracted from 13C-labeled sediment. In the second part of the experiment, groundwater was sampled from pristine ('upstream') and contaminated monitoring wells ('shallow','mid' and 'deep'). DNA was extracted directly from filters (5L of groundwater per well) and shotgun metagenomes were sequenced. This data corresponds with metaproteomic data from Hanson et al., 2015.

PROVIDER: PRJEB22302 | ENA |

REPOSITORIES: ENA

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Project description:Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity. Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.

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	OAOK01.dat.gz	Other
	OAOK01.fasta.gz	Fasta.gz
	OAOK01.master.dat	Other
	OAOL01.dat.gz	Other
	OAOL01.fasta.gz	Fasta.gz

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Tracking carbon-flow from naphthalene degrading bacteria in coal-tar contaminated surface sediments and groundwater.

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