Metatranscriptomic analysis of an iron-rich microbial mat
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR435880.fastq.gz | Fastqsanger.gz | |||
| ERR435899.fastq.gz | Fastqsanger.gz | |||
| ERR435900.fastq.gz | Fastqsanger.gz | |||
| ERR435901.fastq.gz | Fastqsanger.gz | |||
| ERR435902.fastq.gz | Fastqsanger.gz |
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Project description:Pelagic aggregates function as hotspots for microbial activity and biological carbon pumps for exporting OM fixed by photoautotrophs to sediments in lakes and oceans. In iron-rich (ferruginous) lakes, photoferrotrophic or chemolithoautotrophic bacteria appear to contribute to CO2 fixation by oxidizing reduced iron which leads to the formation of iron-rich pelagic aggregates called iron-snow. In acidic lakes, iron snow is colonized mainly by acidophilic iron-cycling microbes that can trigger interspecies aggregation mechanisms. However, the significance of iron oxidizers in carbon fixation, their general role in iron snow functioning, and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis with a 13CO2 metabolic labeling approach to determine general metabolic activities. Protein-based stable isotope probing (protein-SIP) was used to trace the 13CO2 incorporation in iron snow microcosms over time under both oxic and anoxic conditions. Analysis of our mRNA-derived metatranscriptome data identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6%-85.7%) in iron snow encoding a variety of ecologically relevant pathways, including carbon fixation, polysaccharide biosynthesis, and flagellar-based motility. We did not detect transcriptional activity for carbon fixation from archaea or eukaryotes. The largest numbers of expressed genes (3008, 2991, 2936) matched to the genomes of our previously obtained iron snow isolates (Acidithrix sp. C25, Acidiphilium sp. C61, Acidocella sp. C78) separately. 13CO2 incorporation studies identified Leptospirillum and Ferrovum, as the main active chemolithoautotrophs under oxic conditions, and Ferrovum was the main active organism under anoxic conditions as well. Small amounts of labeled 13C (Relative isotope abundance: 1.0%-5.3%) were found in the heterotrophic Acidiphilium and Acidocella. Overall, our data show that iron oxidizers play an important role in the formation of iron minerals and CO2 fixation, but the majority of fixed C apparently did not reach other iron snow microbes. This finding suggests that most of the fixed C will be directly exported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.
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Project description:The phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted from mat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in one diel cycle, and these RNA samples were analyzed by both pyrosequencing and SOLiD technologies. Pyrosequencing was used to assess the community composition, which showed that ~84% of the rRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi and Acidobacteria. Transcription of photosynthesis-related genes conclusively demonstrated the phototrophic nature of two newly discovered populations; these organisms, which were discovered through metagenomics, are currently uncultured and previously undescribed members of Chloroflexi and Chlorobi. Data sets produced by SOLiD sequencing of complementary DNA provided >100-fold greater sequence coverage. The much greater sequencing depth allowed transcripts to be detected from ~15,000 genes and could be used to demonstrate statistically significant differential transcription of thousands of genes. Temporal differences for in situ transcription patterns of photosynthesis-related genes suggested that the six types of chlorophototrophs in the mats may use different strategies for maximizing their solar-energy capture, usage and growth. On the basis of both temporal pattern and transcript abundance, intra-guild gene expression differences were also detected for two populations of the oxygenic photosynthesis guild. This study showed that, when community-relevant genomes and metagenomes are available, SOLiD sequencing technology can be used for metatranscriptomic analyses, and the results suggested that this method can potentially reveal new insights into the ecophysiology of this model microbial community.
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Project description:we analyzed the gene expression profiles of Mat-Lylu cell lines (in duplicate) compared to G cell lines (in duplicate) using Affymetrix tools and dChip software. The objective was to find metastasis-associated genes in prostate cancer, using this in vitro model. Keywords: cell line comparison
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