Project: Relating Microbial Biodiversity to Biological Oceanographic Processes

Despite great strides in our ability to evaluate the composition of marine microbial communities and even aspects of microbial function by molecular genetic techniques, we know very little about how marine microorganisms are distributed and function relate to biological oceanographic processes. This is largely due to the difficulty of integrating molecular biological-based community composition measurements into an oceanographic measurement program, even though recent data imply that microbial diversity should strongly affect many biogeochemical processes. Here we evaluate microbial community diversity in the context of environmental data to provide a first step to linking community structure and processes in the environment. This is a critical first step to relating the potential of molecular genetic techniques to processes that may be represented in conceptual and numerical models of the ocean.

Our laboratories have participated in numerous oceanographic expeditions and programs in recent years, where a comprehensive array of biological oceanographic parameters (physical, chemical, biological, biogeochemical, in situ and satellite optical) was measured. On these cruises we also collected DNA suitable for molecular analysis (at least 265 DNA samples). We analyze that DNA in a reasonably cost-effective manner, by Amplified Ribosomal Intergenic Spacer Analysis (ARISA) fingerprints, backed by clone libraries, to get snapshots of the bacterial community composition suitable for detailed comparisons with the oceanographic datasets. This project is cost effective because we do not request ship time or additional fieldwork, but rather will use existing biological oceanographic data that have been collected at great expense by experts in their specialties.

Most samples are from subtropical or tropical regions. Most of the work focuses on samples from the North Pacific from Hawaii to Empress Seamount (3 cruises), the W Tropical Atlantic including the Amazon Plume, and the San Pedro Ocean Time Series (between Los Angeles and Santa Catalina Island - a warm temperate basin). Molecular and oceanographic data are analyzed by multivariate statistical techniques including ordination, cluster, and canonical analysis. Questions include:
- Do physico-chemical parameters (singly or collectively) structure microbial communities, and if so, how?
- Can we find repeating patterns and seasonality in the composition (especially from our Time Series), and if so, which oceanographic parameters are most closely related to those patterns?
- Which microbial taxa appear together regularly, or are mutually exclusive? Can we use correlations to connect certain taxa to biogeochemical processes?
- Which taxa relate strongly to high or low bacterial or primary production rates or certain phytoplankton groups (including N2 fixers like the cyanobacterium Trichodesmium)?
- Can we better predict bacterial production from primary production (or other properties) if we know what bacterial taxa are present, perhaps in combination with information of phytoplankton types?
- Do certain bacterial taxa relate to distinct optical properties that may be detected by in situ spectroradiometry/transmissometry or possibly even by satellite?

The project includes a significant exploratory component, so it generates numerous specific hypotheses to test later on. Results are data-based (discrete data such as sequences, quantities) and therefore digitally archived; this permits integration with new data on marine microbial diversity as it becomes available, such as from large metagenomics projects that typically do not have the extensive oceanographic data for comparison. We anticipate that our high phylogenetic resolution ITS sequences will permit linking our results with metagenomic data and thus greatly facilitate the oceanographic interpretation of both.

Related files:

Selected Publications:

Fuhrman, J.A., I. Hewson, M.S. Schwalbach, J. Steele, Mark V. Brown, and S. Naeem. 2006. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl. Acad. Sci. USA, 103:13104-13109

Hewson, I, J. A. Steele, D.G. Capone , J.A. Fuhrman. 2006. Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters. Mar. Ecol. Ecol. Ser. 311: 67-77

Hewson, I, J. A. Steele, D.G. Capone , J.A. Fuhrman. 2006. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton community composition. Limnol. Oceanogr. 51: 1274-1283

Hewson, I., D.G. Capone, J. A. Steele, and J.A. Fuhrman. 2006. Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the West Tropical Atlantic. Aquat. Microb. Ecol. 43:11-22

Fuhrman, J.A., J. A. Steele, I. Hewson, M. S. Schwalbach, M.V. Brown, J. L. Green, J. H. Brown. 2008. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Nat. Acad. Sci. USA. 105: 7774-7778

Fuhrman, J.A. and J.A. Steele. 2008. Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat. Microb. Ecol. 53: 69-81

Fuhrman, J.A. 2009. Microbial community structure and its functional implications. Nature. 459: 193-199