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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #347276
Title: Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary

Author
item SMITH, MARIA - Oregon Health & Science University
item HERFORT, LYDIE - Oregon Health & Science University
item Rivers, Adam
item SIMON, HOLLY - Oregon Health & Science University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2019
Publication Date: 11/5/2019
Citation: Smith, M.W., Herfort, L., Rivers, A.R., Simon, H.M. 2019. Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary. Frontiers in Microbiology. Volume 10, Article 2475. https://doi.org/10.3389/fmicb.2019.02475.
DOI: https://doi.org/10.3389/fmicb.2019.02475

Interpretive Summary: Big rivers like the Columbia River move a tremendous amount of soil and organic material to the ocean. In the estuaries where these rivers meet the ocean, the nutrients from the land can cause algae to bloom, but it is less clear what the bacteria in the sediments at the bottom of the estuary are doing. This study looked at the DNA in these estuary sediments to understand what microorganisms are present and what they are doing metabolically. It found that when algae bloom then settle to the bottom of estuary the microbial community shifts to consuming those algae. When less algal material is present, the microbial community shifts towards degrading organic matter from the land.

Technical Abstract: In fast-flowing, river-dominated estuaries, "hotspots" of microbial biogeochemical cycling can be found within areas of extended water retention. Several lateral bays off of the main channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated these regions are both sources and sinks of biogenic particles with potential to impact organic matter fluxes in the estuary. To extend our work, we analyzed 11 sediment metagenomes from three disparate bays: the freshwater Cathlamet Bay, and the brackish Youngs and Baker Bays located nearer the mouth to the south and north of the main channel, respectively. Samples were collected from upper layers of sediments under similar estuarine regimes in August of 2011 and 2013. Sequencing of total DNA and metagenome assembly resulted in >10 Gbp corresponding to >20 million identified coding sequences. All metagenomes were dominated by bacterial sequences, with an abundance of diatom sequences observed in higher salinity samples. Clustering analysis produced four distinct clusters, two of which were characterized by an increased relative abundances of diverse Bacteroidetes, diatom and bacteriophage sequences, suggesting that the diatom bloom degradation stage (early vs. late) was an important factor affecting the bacterial community composition and metabolic potential. In contrast, the other two clusters contained sediment metagenomes with low relative abundance of diatom and Bacteroidetes sequences, and metabolic potential biased towards microbial growth under nutrient limitation. While differences in water salinity clearly influenced the microbial community, our results highlight a central role for labile organic matter (i.e., diatom detritus), in shaping bacterial taxonomic and functional properties in estuarine sediments.