Taxon-specific C/N relative use efficiency for amino acids in an estuarine community

Abstract

Microbial activity plays a critical role in determining the nutrient status of an ecosystem (i.e. N or C limitation). While the balance of C/N assimilation has been measured at the whole community scale, quantitative detection of N and C assimilation from a single substrate at the scale of individual taxa has not been carried out. We recently developed Chip-SIP, a microarray and NanoSIMS-based method for linking microbial phylogeny and function that allows simultaneous measurement of (15)N and (13)C incorporation. Here, we measured the relative incorporation of C and N from dual-labeled substrates by individual microbial taxa in bottle incubations of samples collected from an estuary. Incubation times < 24 h were sufficient to successfully detect active microbes incorporating (15)N ammonium. In subsequent experiments, we used the incorporation of labeled amino acids (AAs) as a proxy for heterotrophic activity and showed different levels of incorporation among different taxonomic groups. Taxon-specific differences in the net incorporation of AA-derived C and N indicate that the C/N relative use efficiency ranged from 0.8 to 1.4, where 1 reflects stoichiometric incorporation of C and N. Our results revealed that microbial organic matter processing is affected by taxon-specific physiological diversity, both in terms of general activity levels and in the ratio of assimilated C/N.

Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

“…Bacteria were enriched in both 13 C and 15 N after incubation with the dual-labeled amino acids, consistent with previous studies (e.g., Mayali et al, 2013). But, in the same incubations, only 15% of the Thaumarchaeal cells enriched in 15 N were also enriched in 13 C. This demonstrates that although they were active, most of the Thaumarchaeota cells did not assimilate carbon from amino acids.…”

Dynamics of Dissolved Organic Nitrogen

“…This result casts doubt on the use of bacterial production estimates, which are largely based on uptake of leucine or thymidine. Following up on that work, Mayali et al (2013) found further evidence of taxon-specific uptake of amino acids in an estuarine system. Additionally, they discovered that Roseobacters incorporated relatively more N and Bacteroidetes relatively more C from an amino acid mixture, potentially because they are selectively incorporating specific components of the mixture.…”

Quantitative Microbial Ecology through Stable Isotope Probing

“…This work advances a quantitative approach to stable isotope probing in order to elucidate taxon-specific processes that drive element cycling in intact communities, bringing to microbial ecology the power of stable isotopes to quantify rates of element fluxes into and through organisms (65,66). Like Chip-SIP (48,67), qSIP provides a means to quantify the ecology of organisms about which we know little more than the genetic fragment used to identify their unique place on the tree of life. These approaches lay the groundwork for a quantitative understanding of microbial ecosystems, including the types of ecological interactions previously described among macroorganisms that influence ecosystem processes.…”