Additional file 3: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

SBML format of the RP model. (XML 1614 kb

Additional file 2: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

RP model and gene knockout results. (XLSX 133 kb

Additional file 1: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

System-level Analyses of robustness of metabolism to environmental and genetic perturbations. (DOCX 3179 kb

Phylogenetic Patterns in the Microbial Response to Resource Availability: Amino Acid Incorporation in San Francisco Bay

<div><p>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.</p></div

Response of taxa targeted by domain-specific (a–c) and genus or order specific (d–f) probes to increasing amino acid concentrations (red = high, blue = medium, green = low).

<p>Data points are for individual probes. Solid lines represent the linear regression and dotted lines are 95% confidence intervals.</p

Pairwise comparisons of isotopic incorporation of ¹⁵N labeled AAs by 107 16S rRNA phylotypes from SF Bay at two concentrations (high, 5 micromolar and low, 50 nanomolar).

<p>Each data point represents the HCE (hybridization corrected enrichment) for a probe set (the slope of delta permil divided by fluorescence). Error bars indicate two standard errors of the slope calculation. The black line represents the linear regression and the blue the 1 to l line.</p

Amino acid incorporation trophic strategies mapped onto a maximum parsimony unrooted 16S rRNA gene phylogeny of taxa from a SF Bay seawater sample.

<p>Ancestral states were identified by parsimony. Asterisks indicate strategies with a statistically clustered distribution indicating a phylogenetic signal.</p

Three different types of microbial responses to resource availability identified by measuring isotopic incorporation of amino acids at High, Medium, and Low concentrations in SF Bay, with the numbers of taxa identified in parentheses.

<p>Three different types of microbial responses to resource availability identified by measuring isotopic incorporation of amino acids at High, Medium, and Low concentrations in SF Bay, with the numbers of taxa identified in parentheses.</p

Ternary plot graphically depicting the ratios of the rRNA phylotype-specific incorporation to varying AA concentrations added to SF Bay water.

<p>Data are color-coded according to the trophic strategies identified in Fig. 3. The position of each data point in relation to the three corners represents the relative contribution of each concentration response.</p

Plant roots alter microbial functional genes supporting litter decomposition

Decomposition of soil organic carbon is central to the global carbon cycle and profoundly affected by plant roots. While root “priming” of decomposition has been extensively investigated, it is not known how plants alter the molecular ecology of soil microbial decomposers. We disentangled the effects of Avena fatua, a common annual grass, on 13C-labeled root litter decomposition and quantified multiple genetic characteristics of soil bacterial and fungal communities. In our study, plants consistently suppressed rates of litter decomposition. Plant uptake N may cause soil microbes under N limitation and reduce their activities. Microbes from planted soils had relatively more genes coding for low molecular weight compound degradation enzymes, while those from unplanted had more macromolecule degradation genes. Higher abundances of “water stress” genes in planted soils suggested plant-induced water stress for microbes. We used a quantitative model to integrate our extensive data set; it indicated that the multiple soil environmental and microbial mechanisms involved in litter decomposition all acted through changing the functional gene profiles of microbial decomposers living near plant roots