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Abstract Predicted shifts in precipitation patterns could impact soil microbial activity, and thereby terrestrial ecosystem functioning. In a Mediterranean grassland soil which had been subjected to contrasting precipitation patterns, we investigated the response of active and inactive bacterial and fungal communities to rewetting over time, using 18O stable isotope probing. Altered precipitation patterns prior to rewetting had little impact on the trajectories over time of the active and inactive bacterial communities after rewetting, as bacteria died or were recruited from the inactive to the active community. The duration of the dry summer conditions affected the diversity and phylogenetic clustering of the inactive microbial community and its functional potential, likely indicating long-lasting effects on ecosystem stability. Highlights • Inactive bacterial community structure changed over time after rewetting. • Precipitation history had little effect on bacterial community trajectories over time. • The diversity of inactive bacterial community changed over time after rewetting. • Active and inactive fungal communities did not differ after rewetting. [ABSTRACT FROM AUTHOR]

Climate influences soil microbial composition and function, but the relative importance of a site's historic climate versus its more immediate environmental conditions is unclear. Using quantitative stable isotope probing (qSIP), we characterized actively growing soil microbial communities and soil properties in three California annual grasslands that span a rainfall gradient and have developed on similar parent material. The soils were assayed in the wet winter season, when environmental conditions are most similar across sites. Since growing populations might be expected to be most responsive to contemporary environmental conditions, we hypothesized that the structure of growing microbial communities would be more similar across the gradient than that of total communities (i.e., including non-growing populations). In addition, we hypothesized that population growth rates would be slowest in the driest site, reflecting a legacy effect of low soil moisture on microbial growth. Soils along the rainfall gradient differed in pH, texture, and cation exchange capacity, but not in total C, C:N or dominant minerals. The radiocarbon (14C) age of soil C (reflecting turnover time) increased with mean annual precipitation but soil respiration was uniformly modern, reflecting microbial reliance on recent C inputs across the sites. The structure of both total and growing microbial communities differed across sites. Across major microbial phyla, including the Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Proteobacteria, bacterial growth rates were consistently lower in the site with the lowest mean annual precipitation. Taxa that were growing at the dry site alone grew more slowly than taxa that grew at multiple sites. These results reflect the influence of climate history and point to the role of environmental filtering at the driest site in shaping its slower growing microbial community, possibly reflecting adaptation to repeated exposure to water stress. Lastly, across taxa, the growth rate of a taxon at one site was correlated with its growth rate in the other sites. This growth rate coherence is likely a consequence of genetically determined physiological traits and is consistent with the idea that evolutionary history constrains growth rate. • Climate strongly influences structure of growing soil microbial communities. • Repeated low water exposure reduces soil microbial growth across taxonomic levels. • Microbial growth rates are consistent between sites across a precipitation gradient. • Genetics and physiology constrain variation in taxon-specific growth rates. [ABSTRACT FROM AUTHOR]

Abstract: We present a significant relationship between the natural abundance isotopic composition of ecosystem pools and the abundance of a microbial gene. Natural abundance 15N of soils and soil DNA were analysed and compared with archaeal ammonia oxidizer abundance along an elevation gradient in northern Arizona and along a substrate age gradient in Hawai'i. There was a significant positive correlation between the abundance of archaeal amoA genes and natural abundance δ15N of total soil or DNA suggesting that ammonia oxidizing archaea play an important role in ecosystem N release. [Copyright &y& Elsevier]

Rewetting dry soils is associated with a burst of microbial activity and mineralization, which manifests itself as a pulse in soil CO 2 emissions, long-known as the Birch effect. In arid and semi-arid systems, soil CO 2 losses upon rewetting at the end of extended dry periods can contribute a significant fraction to the overall carbon (C) budget. Microbial biomass is one of the sources of mineralized C, as was demonstrated over 30 years ago (Kieft et al., 1987). The present paper offers a perspective on how the field has progressed since the 1987 paper was published in Soil Biology & Biochemistry , what it means in terms of current concerns about global climate change, and the needs and potential emphases of future research. Many studies since 1987 have addressed the origin of this CO 2 pulse, finding multiple possible C sources involving both biotic and abiotic processes. We propose that the magnitude of the rewetting event (Δψ) determines the relative contribution from the array of substrates that contribute to the soil CO 2 pulse upon rewetting. The magnitude of the CO 2 pulse is likely related to soil physical characteristics and to the size of the available C pool, which is partly controlled by plants. Further, the relative contributions of the mechanisms generating soil CO 2 pulses upon rewetting are likely to be modified by climate change. To understand and predict the magnitude of soil CO 2 pulses upon rewetting, we advocate continued cross-disciplinary research involving soil microbial ecology, soil physics, soil chemistry, as well as increased integration and recognition of the importance of plant-soil interactions in controlling the soil C pools contributing to soil CO 2 pulses. [ABSTRACT FROM AUTHOR]

Soil microorganisms help transform plant inputs into mineral-associated soil organic carbon (SOC) – the largest and slowest-cycling pool of organic carbon on land. However, the microbial traits that influence this process are widely debated. While current theory and biogeochemical models have settled on carbon-use efficiency (CUE) and growth rate as positive predictors of mineral-associated SOC, empirical tests are sparse, with contradictory observations. Using 13C-labeling of an annual grass (Avena barbata) under two moisture regimes, we found that microbial traits associated with formation of 13C-mineral-associated SOC varied by soil habitat, as did active microbial taxa and SOC chemical composition. In the rhizosphere, bacterial-dominated communities with fast growth, high biomass, and high extracellular polymeric substance (EPS) production were positively associated with 13C-mineral-associated SOC. In contrast, the detritusphere held communities dominated by fungi and more filamentous bacteria, and with greater exoenzyme activity; there, 13C-mineral-associated SOC was associated with slower microbial growth and lower microbial biomass. CUE was a negative predictor of 13C-mineral-associated SOC in both habitats. Using 13C-quantitative stable isotope probing, we found that the majority of 13C assimilation in the rhizosphere and detritusphere at week 12 of the experiment was performed by very few bacterial and fungal taxa (3–5% of the total taxa that assimilated 13C). Several complementary chemical analyses (13C-NMR, FTICR-MS, and STXM-NEXAFS) suggested that SOC in the rhizosphere had a more oxidized chemical signature, while SOC in the detritusphere had a less oxidized, more lignin-like chemical signature. Our findings challenge current theory by demonstrating that microbial traits linked with mineral-associated SOC are not universal, but vary with soil habitat and moisture conditions, and are shaped by a small number of active taxa. Emerging SOC models that explicitly reflect these interactions may better predict SOC storage, since climate change causes shifts in soil moisture regimes and the ratio of living versus decaying roots. • Microbial traits associated with mineral-associated SOC varied by soil habitat. • In the rhizosphere, fast growth and high yield were positively associated with SOC. • The detritusphere community had slower growth and greater exoenzyme activity than the rhizosphere community. • 13C-qSIP showed most C assimilation was performed by very few active taxa. • Chemical composition of SOC was more oxidized in the rhizosphere than the detritusphere. [ABSTRACT FROM AUTHOR]

Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition; however, much of this work has been conducted in marine systems and the factors which shape soil bacterial genomic traits remain largely unknown. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine the environmental parameters that most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, particularly soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, communities in high pH and low soil C:N had smaller genomes and higher GC content—indicating potential resource driven selection against AT base pairs, which have a higher C:N than GC base pairs. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin genome size, and nucleotide and amino acid selection in soil bacteria. • Community averaged genomic traits of 398 soil metagenomes and environmental data. • Average genome size and GC-% negatively correlated, consistent with C limitation. • Correlation between soil C:N and predicted amino acid mean C:N. • Machine learning approach indicated pH strongest driver of genomic traits. [ABSTRACT FROM AUTHOR]