Dataset Information

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

ABSTRACT: Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.

SUBMITTER: Mayali X

PROVIDER: S-EPMC3994146 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

Mayali Xavier X Weber Peter K PK Mabery Shalini S Pett-Ridge Jennifer J

PloS one 20140421 4

Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders o ...[more]

PMID: 24752604

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Project description:Understanding habitat associations is vital for conservation of at-risk marsh-endemic wildlife species, particularly those under threat from sea level rise. We modeled environmental and habitat associations of the marsh-endemic, Federally endangered salt marsh harvest mouse (Reithrodontomys raviventris, RERA) and co-occurrence with eight associated small mammal species from annual trap data, 1998-2014, in six estuarine marshes in North San Francisco Bay, California. Covariates included microhabitat metrics of elevation and vegetation species and cover; and landscape metrics of latitude-longitude, distance to anthropogenic features, and habitat patch size. The dominant cover was pickleweed (Salicornia pacifica) with 86% mean cover and 37 cm mean height, and bare ground with about 10% mean cover. We tested 38 variants of Bayesian network (BN) models to determine covariates that best account for presence of RERA and of all nine small mammal species. Best models had lowest complexity and highest classification accuracy. Among RERA presence models, three best BN models used covariates of latitude-longitude, distance to paved roads, and habitat patch size, with 0% error of false presence, 20% error of false nonpresence, and 20% overall error. The all-species presence models suggested that within the pickleweed marsh environment, RERA are mostly habitat generalists. Accounting for presence of other species did not improve prediction of RERA. Habitat attributes compared between RERA and the next most frequently captured species, California vole (Microtus californicus), suggested substantial habitat overlap, with RERA habitat being somewhat higher in marsh elevation, greater in percent cover of the dominant plant species, closer to urban areas, further from agricultural areas, and, perhaps most significant, larger in continuous size of marsh patch. Findings will inform conservation management of the marsh environment for RERA by identifying best microhabitat elements, landscape attributes, and adverse interspecific interactions.

Dataset Information

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

Publications

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay.

Similar Datasets

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