Climate and the carbon cycle: It is still not clear how global warming will affect the global carbon cycle, either in terms of the magnitude of the effect or even its sign. Help in answering that question will come from long-term field-based experiments designed to explore carbon cycle-climate feedbacks in an ecosystem context. Melillo et al. performed a 26-year soil-warming experiment in a mid-latitude hardwood forest (see the Perspective by Metcalfe). Warming has resulted in a complex pattern of net carbon loss from the soil. These results support projections of a long-term, positive carbon feedback from similar ecosystems as the world warms. Science , this issue p. 101 ; See also p. 41

Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

Low-molecular-weight organic compounds in root exudates play a key role in plant–microorganism interactions by influencing the structure and function

Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5oC above ambient temperatures for 5, 8 and 20 years. We used this chronosequence to examine soil microbial communities in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 10% to 2% relative abundance with warming. We also observed a significant decrease in mean bacterial ribosomal RNA gene copy number in warming plots compared to controls, a trait linked to maximum growth rate or trophic strategy among bacteria. Increased bacterial alpha diversity, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria suggest that more or alternative niche space is being created over the course of long-term warming.