Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

Abstract

Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with N. Following incubation with NH4+, distinct patterns of N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased N use by Firmicutes and Bacteriodetes. While NH4+ is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.

Phylogenetic conservation of soil bacterial responses to simulated global changes

“…A critical next step, however, is to connect shifts in community composition to the functional processes soil bacteria carry out. Many potential functions (as predicted through genomic traits) are phylogenetically conserved [4,74], and new techniques estimating taxon-specific process rates find that these measures are also phylogenetically patterned [10,19]. Finally, recent evidence suggests that phylogeny has a stronger effect than the environment on bacterial processes such as growth rate and carbon assimilation [76].…”

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

“…The BM assigns a value of 0 to indicate phylogenetic independence (random phylogenetic distribution of traits) and values close to 1 for a strong phylogenetic signal (nonrandom phylogenetic distribution of traits). These tests were used in previous qSIP studies to assign putative ecological functions to specific phylogenetic clades (25, 71, 72). …”

Quantitative stable isotope probing with H218O to measure taxon‐specific microbial growth

“…Quantitative SIP has other advantages as well. Mathematical approaches have been developed in which qSIP data can be modeled to estimate growth, turnover, and mortality for all taxa in a sample (Koch et al, 2018). Quantitative SIP with H 2 18 O can be performed in parallel with incubations of other labeled substrates to look at differences in growth when substrates (e.g., glucose) are present (Morrissey et al, 2016(Morrissey et al, , 2018.…”

“…Specificity and sensitivity of these improved SIP analyses have been discussed elsewhere (Youngblut, Barnett, & Buckley, 2018b). Quantitative SIP has an advantage by quantifying the degree of isotopic enrichment for individual taxa and using that value to infer a quantitative measure of population growth (Hungate et al, 2015;Koch et al, 2018).…”