Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria

Abstract

Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

“…Quantitative stable-isotope probing (qSIP) and techniques such as “high-resolution” SIP (HR-SIP) [ 19 ] are expansions of the original SIP concept that combine density gradient ultracentrifugation with mathematical models designed to improve the quantification of isotope enrichment [ 6 , 20 ]. qSIP enables taxon-specific estimates of isotope enrichment and substrate consumption (using 13 C and 15 N) [ 21 , 22 ], as well as cell growth and mortality rates of individual taxa (using 18 O-enriched water) [ 23 – 25 ]. Recent qSIP studies have used the method to illustrate how wild microbial communities are shaped by evolutionary history [ 26 , 27 ], soil temperature and warming [ 28 , 29 ], amendments of water and nutrients [ 18 , 30 ], and trophic relationships among bacterial predators and their prey [ 31 ].…”

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

“…Figure 4). A similar amount of variation in CUE was explained by phylogeny at class level (20%), relative to substrate class (15%, Table 1), indicating that interactions between substrate traits (e.g., mean differences in molecular size and nominal oxidation state of C among substrate classes) and microbial traits (e.g., transporter gene frequencies, protein synthesis efficiency, relative maintenance costs) provide a strong foundation for this aspect of soil bacterial ecology [40,41].…”

Life history strategies among soil bacteria—dichotomy for few, continuum for many

“…In keeping with other ecological frameworks (e.g., C-S-R and Y-A-S [ 10 , 48 ]), stress treatments are a priority for future studies in order to understand the diversity of stress tolerance strategies and their effect on growth. The utilization of both simple and complex nutrient sources across the community (as well as from both plant and microbial origin) will also be a key point of inquiry, and designs that explore this difference will refine our thinking of microbial ecology in the soil realm (e.g., Dang et al [ 49 ]). Lastly, the relatively short timescales inherent to nutrient pulse-type experiments mean that such incubations must be placed into longer-term studies strategically.…”