Microbial Physiology

Abstract: Microbes are key drivers of the world's ecosystems. The vast majority of the world's diversity and metabolic potential lies within micro-organisms, yet with the advent of molecular-scale observation, we are still barely beginning to understand this microscopic resource. The expanded second edition provides a detailed description of the methods that have made microbial ecology possible.

Abstract: The loss of carbon dioxide from soils increases initially under climate warming, but tends to decline to control levels within a few years. Simulations of the soil-carbon response to warming with a microbial-enzyme model show that a decline in both microbial biomass and the production of degrading enzymes can explain this attenuation response. Most ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon, producing a positive feedback to rising global temperatures1,2. Although field experiments document an initial increase in the loss of CO2 from soils in response to warming, in line with these predictions, the carbon dioxide loss from soils tends to decline to control levels within a few years3,4,5. This attenuation response could result from changes in microbial physiological properties with increasing temperature, such as a decline in the fraction of assimilated carbon that is allocated to growth, termed carbon-use efficiency6. Here we explore these mechanisms using a microbial-enzyme model to simulate the responses of soil carbon to warming by 5 ∘C. We find that declines in microbial biomass and degradative enzymes can explain the observed attenuation of soil-carbon emissions in response to warming. Specifically, reduced carbon-use efficiency limits the biomass of microbial decomposers and mitigates the loss of soil carbon. However, microbial adaptation or a change in microbial communities could lead to an upward adjustment of the efficiency of carbon use, counteracting the decline in microbial biomass and accelerating soil-carbon loss. We conclude that the soil-carbon response to climate warming depends on the efficiency of soil microbes in using carbon.

Abstract: Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production. Soil microbes process plant remnants and are hypothesized to synthesize soil organic matter (SOM). Here, Kallenbach and colleagues directly measure chemically diverse and stable SOM derived from microbial communities in the absence of plant compounds.

Abstract: The recent application of molecular phylogeny to environmental samples has resulted in the discovery of an abundance of unique and previously unrecognized microorganisms. The vast majority of this microbial diversity has proved refractory to cultivation. Here, we describe a universal method that provides access to this immense reservoir of untapped microbial diversity. This technique combines encapsulation of cells in gel microdroplets for massively parallel microbial cultivation under low nutrient flux conditions, followed by flow cytometry to detect microdroplets containing microcolonies. The ability to grow and study previously uncultured organisms in pure culture will enhance our understanding of microbial physiology and metabolic adaptation and will provide new sources of microbial metabolites. We show that this technology can be applied to samples from several different environments, including seawater and soil.