Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

Abstract

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that average apparent generation times in soil are quite slow (20 to 64 days) but also highly variable at the compound-specific level (6 to 1137 days), suggesting differential growth rates between community subsets. We observe that low-biomass communities can exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions

“…Therefore, to accurately estimate microbial fatty acid production the physiological parameter ‘water hydrogen assimilation constant (a w )’ should be applied ( 74 , 75 ), obtained from the regression of the 2 H isotopic composition of fatty acids and water source. In a recent survey it was demonstrated that a w can range from values close to 0.1 up to values close to 1 ( 76 ). In complex communities, such as soil, the assimilation constant is difficult to estimate, but assuming all microbes are heterotrophs, this value is on average 0.71 ( 35 ), which we also applied in this study.…”

“…Deuterium ( 2 H) incorporation into fatty acids can serve as an alternative SIP approach to measure microbial growth, as all microorganisms synthesize lipids and fatty acids to build and maintain cell membranes regardless of their metabolic activity and cell cycle stage. 2 H-labelling has been used in single cell studies ( 33 ), pure cultures ( 34 ) and soil microbial communities ( 35 ). Lipids likely require less investment into repair mechanisms compared to nucleic acids or proteins, which can be resynthesized during repair and cellular maintenance potentially affecting growth rates calculation ( 35 , 36 ), and provide a precise measure of microbial membrane production rates and cell growth.…”

“…2 H-labelling has been used in single cell studies ( 33 ), pure cultures ( 34 ) and soil microbial communities ( 35 ). Lipids likely require less investment into repair mechanisms compared to nucleic acids or proteins, which can be resynthesized during repair and cellular maintenance potentially affecting growth rates calculation ( 35 , 36 ), and provide a precise measure of microbial membrane production rates and cell growth. The major advantages of tracing 2 H into fatty acids ( 2 H-PLFA-SIP) are that it allows the simultaneous and sensitive quantification of bacterial and fungal replication rates ( 37 ) and the concurrent measurement of storage compound production ( 38 ).…”

How do soil microbes shape ecosystem biogeochemistry in the context of global change?

“…Although long‐term in vitro microbial evolution experiments have shown strong evidence for adaptation (Lenski, 2017; Rainey & Travisano, 1998; Rodríguez‐Verdugo, 2021; Travisano & Lenski, 1996), it is unclear if these observations extend to natural systems (Koskella & Vos, 2015). In the few examples investigating the impact of evolution within natural communities, it appears that slow generation times (Caro et al, 2022) combined with high spatial heterogeneity may limit detection of genome evolution and result in different evolutionary dynamics than those observed in laboratory environments (Chase et al, 2021). Resolving the feedbacks between ecological and evolutionary processes will be essential for improving model predictions of biogeochemical functions, and might contradict the current belief that biodiversity inhibits evolutionary responses to changing environments (de Mazancourt et al, 2008; Johansson, 2008; Loeuille & Leibold, 2008).…”

Temperature adaptation of soil bacterial communities across the Arctic

“…A novel approach to modeling community-wide temperature responses of soil bacteria using thermal niche theory 141 5 (Nottingham et al, 2021). Current estimates of turnover times for bacterial community biomass vary largely from 2 to 169 days (Caro et al, 2022). The large deviation in growth rates might be explained by other environmental factors such as soil moisture, plant-soil interactions, pH, substrate quantity and quality (Rousk and Bååth, 2011), which means that implementing growth rates into our model would like require more environmental data about the soils.…”