Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms

Abstract

Summary Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent (‘decoupled’) axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.

Transport‐limited reactions in microbial systems

“…We have presented evidence that the FRT limit applies to multiple important metabolic pathways in the Cariaco Basin redoxcline, a system whose microbiology has been the topic of intense investigations for decades (Hashimoto et al, 1983;Muller-Karger et al, 2019;Reeburgh, 1976). The FRT limit can thus help explain the decoupling between microbial taxonomic variation and function, frequently reported for marine and other aquatic systems (Coles et al, 2017;Louca et al, 2020;Louca, Parfrey, & Doebeli, 2016;Ramírez-Flandes et al, 2019). Comparison of data to FRT models can also help distinguish diffusion-limited from kinetically limited reactions and thus help prioritize costly efforts to determine kinetic parameters.…”

Microbiology of Big Soda Lake, a multi‐extreme meromictic volcanic crater lake in the Nevada desert

“…Most of the OTUs and ASVs that dominated the anoxic BSL samples (e.g., OTU.110 in the ML635J‐40 aquatic group or OTU.100 in the Dethiobacteraceae family) were rare or even non‐existent in the LSL samples, and vice versa (Figures S2 and S3B–F). These community differences between the two anoxic water columns are likely at least partly driven by their difference in salinity, as the latter is a known strong factor shaping aquatic prokaryotic communities (Louca et al, 2020). Further, among the abundant ASVs (proportion ≥0.001 in at least one sample), a strong phylogenetic clustering was observed by lake, that is, ASVs belonging to the same OTU were largely restricted to the same lake (Figure S4).…”

EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

“…EasyAmplicon does not cover all the functions required for microbiome analysis. There are currently some mainstream and very distinctive microbiome analysis tools, such as STAMP [26], LEfSe [27], PICRUSt 1 & 2 [28,29], BugBase [30], FAPROTAX [31], and iTOL [33]. However, some input files are difficult to prepare for users without bioinformatics backgrounds.…”

“…Currently, it provides more than 20 and allow personalized modification. In addition, it also generates standard input for the most popular software, such as STAMP [26], LEfSe [27], PICRUSt 1 & 2 [28,29], BugBase [30], FAPROTAX [31], ImageGP [32], and iTOL [33]. EasyAmplicon provides a free, reproducible, and personalized solution for amplicon analysis, which could be an amazing software tool for microbiome research.…”