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Title: Integrated metagenomic and metaproteomic analyses of marine biofilm communities

item LESKI, TOMASZ - Naval Research Laboratory
item Li, Robert
item HERVEY, JUDSON - Naval Research Laboratory
item LEBEDEV, NIKOLAI - Naval Research Laboratory
item HAMDAN, LEILA - Naval Research Laboratory
item WANG, ZHENG - Naval Research Laboratory
item DESCHAMPS, JEFFREY - Naval Research Laboratory
item KUSTERBECK, ANNE - Naval Research Laboratory
item VORA, GARY - Naval Research Laboratory

Submitted to: BIOFOULING
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2014
Publication Date: 11/19/2014
Citation: Leski, T.A., Li, R.W., Hervey, J.W., Lebedev, N., Hamdan, L.J., Wang, Z., Deschamps, J.R., Kusterbeck, A.W., Vora, G.J. 2014. Integrated metagenomic and metaproteomic analyses of marine biofilm communities. BIOFOULING. 30:10, 1211-1223. DOI:10.1080/08927014.2014.977267.

Interpretive Summary: Microbial communities play a critical role in global biogeochemical cycling. The vast majority of bacteria on our planet reside in biofilm communities. Despite the known impact that biofilms have on agriculture, industrial processes, medicine, and the materials industry, our understanding of these natural microbial assemblages has been limited by a lack of analytical tools that are capable of deconvoluting and measuring their inherent complexity. In this study, we utilized multiple advanced technologies, such as PhyloChip microbial profiling, metagenomic sequencing, qualitative and quantitative nano-liquid chromatography, tandem mass spectrometry metaproteomic analyses, elemental analyses, and fluorescence spectroscopy to understand the role different geographic environments play in determining the composition and function of ship hull air-water interface marine biofilms. Our integrated data promote a better understanding of the environmental variables, temporal dynamics and microbe-microbe interactions that determine the formation, composition and function of complex biofilm communities, which will lead to a better design of anti-fouling materials for broad applications in agriculture, medicine and industrial manufacturing.

Technical Abstract: Metagenomic and metaproteomic analyses were utilized to begin to understand the role varying environments play on the composition and function of complex air-water interface biofilms sampled from the hulls of two ships that were deployed in different geographic waters. Prokaryotic community analyses using PhyloChip-based 16S rDNA profiling revealed two significantly different and taxonomically diverse biofilm communities with the majority of OTUs assigned to members of the Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes and 4101 taxa with significant inter-ship abundance differences. Although metagenomic sequencing indicated that both biofilms were dominated by prokaryotic sequence reads (>91%), the ship-1 metagenome harbored greater organismal and functional diversity and was comparatively enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic eukaryotes whereas the ship-2 metagenome was enriched for sequences from Proteobacteria and microscopic photosynthetic eukaryotes. Qualitative LC-MS/MS metaproteome analyses using the same biofilms identified 678 unique proteins, revealed little overlap in species and protein composition and contrasted with the metagenomic findings in that ~80% of the classified and annotated proteins were found to be of eukaryotic origin and dominated by members of the Bacillariophyta, Cnidaria, Chordata and Arthropoda. Within the shared metaproteome, quantitative analyses demonstrated a significantly greater abundance of structural proteins from macroscopic eukaryotes on ship-1 and diatom photosynthesis proteins on ship-2. Finally, photosynthetic pigment and elemental analyses confirmed that both biofilms were the result of phototrophic processes. Taken together, the data promote a better understanding of the organismal and biomolecular composition of marine biofilm communities and highlight caveats in the interpretation of stand-alone environmental ‘omics’ datasets.