Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands

Gihring, Thomas M., Mike Humphrys, Heath J. Mills, Markus Huettel, Joel E. Kostka

Limnol. Oceanogr., 54(4), 2009, 1073-1083 | DOI: 10.4319/lo.2009.54.4.1073

ABSTRACT: We identified microbial taxa that catalyze phytodetritus degradation and denitrification in permeable coastal sediments of the northeast Gulf of Mexico. Stable isotope probing experiments were used to track the assimilation of isotopically labeled substrate into bacterial deoxyribonucleic acid (DNA) and directly link the taxonomic identification of benthic microorganisms with particulate organic matter degradation and denitrification activity. Phytodetritus deposition events were simulated in the laboratory by the addition of 13C-enriched, heat-killed Spirulina cells to intact sediment core incubations. Immediate increases in O2 consumption (3-fold), N2 efflux (16-fold), and dissolved inorganic nitrogen efflux were observed after phytodetritus addition relative to unamended treatments, suggesting that the benthic microbial community was poised to immediately begin oxidizing deposited organic matter. Analyses of 16S ribosomal ribonucleic acid gene sequences amplified from 13C-enriched DNA fractions demonstrated that members of the Gammaproteobacteria (Vibrionales and Alteromonadales), Deltaproteobacteria, Actinobacteria, Verrucomicrobia, and Planctomycetes metabolized the phytodetritus amendment. Terminal restriction length polymorphism analyses showed increases in the relative abundance of Gammaproteobacteria, Planctomycetes, and Bacteroidetes with phytodetritus addition. Alphaproteobacteria were identified as metabolically active denitrifiers by phylogenetic analysis of nitrous oxide reductase gene sequences from 13C-enriched DNA fractions. This study provides the first identification of microorganisms responsible for organic matter degradation in marine sediments by DNA sequence analysis. Microbial assemblages recognized for high-molecular-weight organic matter oxidation in the marine water column were important in catalyzing these processes in permeable sediments.

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