Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.

Autor:	Mosier AC; Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA., Miller CS; Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA., Frischkorn KR; Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA., Ohm RA; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Li Z; Oak Ridge National LaboratoryOak Ridge, TN, USA; Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National LaboratoryKnoxville, TN, USA., LaButti K; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Lapidus A; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Lipzen A; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Chen C; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Johnson J; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Lindquist EA; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Pan C; Oak Ridge National Laboratory Oak Ridge, TN, USA., Hettich RL; Oak Ridge National Laboratory Oak Ridge, TN, USA., Grigoriev IV; US Department of Energy Joint Genome Institute Walnut Creek, CA, USA., Singer SW; Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA., Banfield JF; Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2016 Mar 03; Vol. 7, pp. 238. Date of Electronic Publication: 2016 Mar 03 (Print Publication: 2016).
DOI:	10.3389/fmicb.2016.00238
Abstrakt:	The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.
Databáze:	MEDLINE
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