MicroTOOLs microarray and analysis pipeline
MicroTOOLs microarray is an environmental microarray that targets thousands of functional genes in marine pelagic microorganisms. The design of this microarray was a multi-institutional effort and includes “favorite” genes and organisms from many labs. The design approach involved collecting a set of genes - known molecular markers for ecologically important processes in the oceans - and searching for their orthologs within marine microbial genomes, PCR amplicons, metagenomes and metatranscriptomes. Several probes were designed for each marker gene for highly specific detection. The marker genes include genes for nutrient and oxidative stress responses, carbon, nitrogen, phosphorus, sulfur and iron transport and metabolisms, DNA replication and other cell processes. Besides bacterial, archaeal and eukaryotic, viral genes were also targeted.
The microarray design is flexible, easy to upgrade as new nucleotide sequence information becomes available, and the approach can be applied for other environmental sites. We have recently developed a software pipeline to support the analysis of MicroTOOLs microarrays. The pipeline automates the initial analysis of new arrays, from quality filtering and normalization to the detection of differentially expressed genes and gene expression networks (WGCNA).
Click here for the MicroTOOLs software and a demonstration of the pipeline:
Transcriptional responses of microbial community in the transitional zone of the California Current System (CCS). Top left panel: The whole microbial community from a station in the transitional zone was diluted with water, rich in nutrients, from the same station (pink), oligotrophic water from a station in the CCS (blue) and oligotrophic water with addition of nitrate (green). Bottom left panel: nutrient addition had highest number of genes up-regulated in comparison to the control (no dilution). Bottom right panel: distribution of transcriptional responses and phylogeny of genes up-regulated in the nutrient rich treatment. Top right panel: SAR11 genes up-regulated in the nutrient addition. The star indicates genes with significantly differential transcription among treatments.
Assesing active transcription in marine microbes using the MicroTOOLs microarray
We applied the microarray approach to study responses of microbial community to nutrient inputs. At Station ALOHA, addition of iron resulted in a relief of iron stress followed by increased energy metabolism and also nitrogen limitation in Prochlorococcus and oligotrophic strains of Synechococcus (Shilova et al., 2014). In California Current System, Alphaproteobactera SAR11 clade responded to the addition of nutrient rich water with increased transcriptional activity of genes encoding proteorhodopsin, dimethylsulphoniopropionate and phosphonate assimilation (see figure to the left).
The MicroTOOLs microarray can facilitate understanding of the mechanisms underlying changes in metabolic and physiological states of individual microbial taxa in response to nutrient input and other environmental stimuli. This has implications in advancing marine microbial ecology and modeling anthropological impacts on marine ecosystems.