Showing papers by "Jane C. Marks published in 2015"

Quantitative Microbial Ecology through Stable Isotope Probing

Abstract: Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

Linking soil bacterial biodiversity and soil carbon stability

Abstract: Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this ‘priming’ effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis

Abstract: The efficiency with which microbes use substrate (Carbon Use Efficiency or CUE) to make new microbial biomass is an important variable in soil and ecosystem C cycling models. It is generally assumed that CUE of microbial activity in soils is low, however measured values vary widely. It is hypothesized that high values of CUE observed in especially short-term incubations reflect the build-up of storage compounds in response to a sudden increase in substrate availability and are therefore not representative of CUE of microbial activity in unamended soil. To test this hypothesis, we measured the 13CO2 release from six position-specific 13C-labeled glucose isotopomers in ponderosa pine and pinon-juniper soil. We compared this position-specific CO2 production pattern with patterns expected for 1) balanced microbial growth (synthesis of all compounds needed to build new microbial cells) at a low, medium, or high CUE, and 2) synthesis of storage compounds (glycogen, tri-palmitoyl-glycerol, and polyhydroxybutyrate). Results of this study show that synthesis of storage compounds is not responsible for the observed high CUE. Instead, it is the position-specific CO2 production expected for balanced growth and high CUE that best matches the observed CO2 production pattern in these two soils. Comparison with published studies suggests that the amount of glucose added in this study is too low and the duration of the experiment too short to affect microbial metabolism. We conclude that the hypothesis of high CUE in undisturbed soil microbial communities remains viable and worthy of further testing.

Leaf-litter leachate is distinct in optical properties and bioavailability to stream heterotrophs

Abstract: Dissolved organic C (DOC) leached from leaf litter contributes to the C pool of stream ecosystems and affects C cycling in streams. We studied how differences in leaf-litter chemistry affect the optical properties and decomposition of DOC. We used 2 species of cottonwoods (Populus) and their naturally occurring hybrids that differ in leaf-litter phytochemistry and decomposition rate. We measured DOC and nutrient concentration in leaf leachates and determined the effect of DOC quality on heterotrophic respiration in 24-h incubations with stream sediments. Differences in DOC composition and quality were characterized with fluorescence spectroscopy. Rapidly decomposing leaves with lower tannin and lignin concentrations leached ∼40 to 50% more DOC and total dissolved N than did slowly decomposing leaves. Rates of heterotrophic respiration were 25 to 50% higher on leachate from rapidly decomposing leaf types. Rates of heterotrophic respiration were related to metrics of aromaticity. Specifically, rates...

Closely Related Tree Species Differentially Influence the Transfer of Carbon and Nitrogen from Leaf Litter Up the Aquatic Food Web

Abstract: Decomposing leaf litter in streams provides habitat and nutrition for aquatic insects. Despite large differences in the nutritional qualities of litter among different plant species, their effects on aquatic insects are often difficult to detect. We evaluated how leaf litter of two dominant riparian species (Populus fremontii and P. angustifolia) influenced carbon and nitrogen assimilation by aquatic insect communities, quantifying assimilation rates using stable isotope tracers (13C, 15N). We tested the hypothesis that element fluxes from litter of different plant species better define aquatic insect community structure than insect relative abundances, which often fail. We found that (1) functional communities (defined by fluxes of carbon and nitrogen from leaf litter to insects) were different between leaf litter species, whereas more traditional insect communities (defined by relativized taxa abundances) were not different between leaf litter species, (2) insects assimilated N, but not C, at a higher rate from P. angustifolia litter compared to P. fremontii, even though P. angustifolia decomposes more slowly, and (3) the C:N ratio of material assimilated by aquatic insects was lower for P. angustifolia compared to P. fremontii, indicating higher nutritional quality, despite similar initial litter C:N ratios. These findings provide new evidence for the effects of terrestrial plant species on aquatic ecosystems via their direct influence on the transfer of elements up the food web. We demonstrate how isotopically labeled leaf litter can be used to assess the functioning of insect communities, uncovering patterns undetected by traditional approaches and improving our understanding of the association between food web structure and element cycling.