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Study

Study Name: Acid Mine Drainage (AMD) fungal community from Richmond mine, Iron Mountain, CA

Projects

Biosamples

Organisms

Biosamples: 4 Seq. Projects: 16
STUDY INFORMATION
GOLD Study ID Gs0111523
Study Name Acid Mine Drainage (AMD) fungal community from Richmond mine, Iron Mountain, CA
Other Names In situ expression of acidic and thermophilic carbohydrate active enzymes by filamentous fungi
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id SRP120972  (Link to NCBI )
Study Title Acidomyces richmondensis microbial communities from an AMD in Iron Mountain, California, USA - streamer biofilm Metatranscriptome - polyA selected metatranscriptome
Study Abstract
  
SRA Study Id SRP099250  (Link to NCBI )
Study Title Acidomyces richmondensis microbial communities from an AMD in Iron Mountain, California, USA - streamer biofilm Metatranscriptome - ribo0 n/a metatranscriptome
Study Abstract
  
SRA Study Id SRP120969  (Link to NCBI )
Study Title Acidomyces richmondensis microbial communities from an AMD in Iron Mountain, California, USA - floating biofilm Metatranscriptome - polyA selected metatranscriptome
Study Abstract
  
SRA Study Id SRP099256  (Link to NCBI )
Study Title Acidomyces richmondensis microbial communities from an AMD in Iron Mountain, California, USA - floating biofilm Metatranscriptome - ribo0 n/a metatranscriptome
Study Abstract
  
Legacy ER Study ID 39163
Legacy GOLD ID Gm0039163
Added By Ionna Pagani on 2012-12-21
Last Modified By Tatiparthi Reddy on 2014-01-02
PI Steven W. Singer
Description We are using acid mine drainage (AMD) biofilms from Iron Mountain Mine?a well-characterized model system (e.g., Denef et al. 2010 and references therein)?to develop approaches to systematically examine carbon cycling in communities at the molecular level. The low-complexity AMD microbial community shifts from primary production in early growth stages to a mixture of heterotrophic and autotrophic metabolisms in the later stages of development, making it an ideal system to examine the flow of carbon into and through the system. Surveys of phylogenetic marker genes and fluorescent in situ hybridization microscopy showed that a variety of Eukaryotes, including protists and filamentous fungi, co-occur with a mix of acidophilic Bacteria, Archaea, and Viruses in late developmental stage floating and streamer biofilm communities (Baker et al. 2004; Baker et al. 2009). These eukaryotes likely play an important role in recycling organic carbon within the biofilms. The dominant eukaryotic species in AMD biofilms is the filamentous fungus Acidomyces richmondensis (in the Dothideomycetes class of the Ascomycota phylum). Secreted A. richmondensis enzymes have adapted to the extremely acidic (pH 5000) are also detected in the metaproteome, confirming in situ expression. Among the most highly expressed GH families (based on transcript and protein abundance) are those that hydrolyze the sugars mannose, xylan, and galactose, which have been shown to be constituents of the extracellular matrix in the AMD biofilm (Jiao et al. 2010). In the proposed work, we aim to further evaluate the involvement of eukaryotic CAZymes, including GHs and cellulases, in AMD carbon cycling by examining their expression under different growth conditions both in situ and in vitro. Our current expression data (described above) includes transcriptomics from one fungal streamer biofilm sample (with no replication) and proteomics of a fungal streamer biofilm at a different site and time point (also without replication). We propose to expand this dataset to include community transcriptomics and proteomics (with replication) in two different types of biofilms where A. richmondensis may exhibit different growth strategies: the common floating biofilms and the more specialized fungal streamer biofilms found in high-flow portions of the AMD. We will identify the expression of CAZymes likely secreted from the cell (based on analysis of sequence signatures such as SignalP), suggestive of in situ expression at high temperature and low pH typical of the AMD environment. We will also use transcriptomics of A. richmondensis cultures to determine which genes are upregulated when grown with different substrates (e.g., cellulose and glucose). We will use existing meta-genomic and proteomic data to identify which community members have the genetic potential to produce the sugars consumed by A. richmondensis (e.g., the most abundant organism in the biofilm, Leptospirillum, likely produces cellulose). Together, this analysis will link functional activities encoded and expressed by fungi with biogeochemical processes within the ecosystem.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Aquatic
Ecosystem Type Freshwater
Ecosystem Subtype Groundwater
Specific Ecosystem Acid Mine Drainage
STUDY COMPOSITION
Number of Biosamples 4
Number of Organisms 1
Number of Seq Projects 16
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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