TY - JOUR

T1 - Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

AU - Mosier, Annika C.

AU - Miller, Christopher S.

AU - Frischkorn, Kyle R.

AU - Ohm, Robin A.

AU - Li, Zhou

AU - LaButti, Kurt

AU - Lapidus, Alla

AU - Lipzen, Anna

AU - Chen, Cindy

AU - Johnson, Jenifer

AU - Lindquist, Erika A.

AU - Pan, Chongle

AU - Hettich, Robert L.

AU - Grigoriev, Igor V.

AU - Singer, Steven W.

AU - Banfield, Jillian F.

PY - 2016/3/3

Y1 - 2016/3/3

N2 - 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.

AB - 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.

KW - Biofilm

KW - Carbon

KW - Fungi

KW - Metagenomics

KW - Nitrogen

KW - Proteomics

KW - Transcriptomics

UR - http://www.mendeley.com/research/fungi-contribute-critical-spatially-varying-roles-nitrogen-carbon-cycling-acid-mine-drainage

U2 - 10.3389/fmicb.2016.00238

DO - 10.3389/fmicb.2016.00238

M3 - Article

C2 - 26973616

VL - 7

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

ER -