Advancing our understanding of the oxygen minimum zone microbial communities by an integrated metatranscriptomics approach

- The article describes about an integrated metatranscriptomic pipeline that can be used to analyze data from any environmental sample.
- IDBA-UD can assemble short read sequencing data with highly uneven sequencing depth without reference sequences.
- Kaiju was used for taxonomic classification while COGNIZER was used for function annotation using multiple databases.
- The dynamic biodiversity in deep-sea water reveals that bacteria are dominant over archaea.

OMZ (Oxygen Minimum Zone) is the zone in which oxygen saturation in sea water is at the lowest and this zone occurs at depths of around 100-1000 m. Although oxygen concentration is low and condition is very harsh for survival of microbes in OMZ regions, still these regions harbor a large number of microbes, probably surviving by anaerobic metabolic pathways. Thus, we investigated one of the SRA (Sequence Read Archive) OMZ data of North Pacific deep-sea water with an integrative metatranscriptomics approach. We performed de novo metatranscriptome assembly of 9,376,032 high quality reads which were assembled into 92,182 contigs yielding a total 69,414 genes. We here predicted reliable taxonomy and functional annotation by integrating several bioinformatics annotation tools such as Kaiju and COGNIZER. COGNIZER works by cross-mapping sequences with different databases and the number of gene-hits produced with each database are GO 14080 (20.38%), KEGG 10689 (15.39%), PFAM 9649 (13.90%), COG 9347 (13.46%), FIG 6586 (9.48%). We have also executed BLASTP analysis locally (67% annotated) and altogether the functional annotations performed by integrative metatranscriptomic approaches should considerably enhance the percentage of annotated genes. Within the prokaryotic community, bacteria is dominant over archaeal phyla. On the other hand from the eukaryotic community decreased abundance of fungi and algae in deep-sea dataset was observed. From KEGG pathway study, it can be concluded that microbes at OMZ regions are involved in biogeochemical nitrogen cycle by the help of ammonia oxidizing bacteria and ammonia oxidizing archaea. Overall, the metatranscriptomics analysis will provide useful information of microbial composition and functional study in deep-sea environment.