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There is an emerging consensus that microbial necromass carbon is the primary constituent of stable soil carbon, yet the controls on the stabilization process are unknown. Prior to stabilization, microbial necromass may be recycled by the microbial community. We propose that the efficiency of this recycling is a critical determinant of soil carbon stabilization rates. Here we explore the controls on necromass recycling efficiency in 27 UK grassland soils using stable isotope tracing and indicator species analysis. We found that recycling efficiency was unaffected by land management. Instead, recycling efficiency increased with microbial growth rate on necromass, and was highest in soils with low historical precipitation. We identified bacterial and fungal indicators of necromass recycling efficiency, which could be used to clarify soil carbon stabilization mechanisms. We conclude that environmental and microbial controls have a strong influence on necromass recycling, and suggest that this, in turn, influences soil carbon stabilization.Microbial necromass recycling, which can influence soil carbon stabilization, is controlled by microbial growth and precipitation, as indicated by stable isotope tracing and indicator species analysis in a range of UK grasslands.

Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates. Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.

Mountain soils stock large quantities of carbon as particulate organic matter that may be highly vulnerable to climate change. To explore potential shifts in soil organic matter (SOM) form and stability under climate change (warming and reduced precipitations), we studied the dynamics of SOM pools of a mountain grassland in the Swiss Jura as part of a climate manipulation experiment. The climate manipulation (elevational soil transplantation) was set up in October 2009 and simulated two realistic climate change scenarios. After 4 years of manipulation, we performed SOM physical fractionation to extract SOM fractions corresponding to specific turnover rates, in winter and in summer. Soil organic matter fraction chemistry was studied with ultraviolet, 3D fluorescence, and mid-infrared spectroscopies. The most labile SOM fractions showed high intra-annual dynamics (amounts and chemistry) mediated via the seasonal changes of fresh plant debris inputs and confirming their high contribution to the microbial loop. Our climate change manipulation modified the chemical differences between free and intra-aggregate organic matter, suggesting a modification of soil macro-aggregates dynamics. Interestingly, the 4-year climate manipulation affected directly the SOM dynamics, with a decrease in organic C bulk soil content, resulting from significant C-losses in the mineral-associated SOM fraction (MAOM), the most stable form of SOM. This SOC decrease was associated with a decrease in clay content, above- and belowground plants biomass, soil microbial biomass and activity. The combination of these climate changes effects on the plant–soil system could have led to increase C-losses from the MAOM fraction through clay-SOM washing out and DOC leaching in this subalpine grassland.

1. Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied and consequently poorly understood. 2. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential methane production (PMP) and oxidation (PMO) in two microhabitats (lawns and hummocks). 3. Whilst PFT removal only marginally altered the peat organic matter chemistry, we observed considerable changes in microbial community structure. This resulted in altered PMP and PMO. PMP was slightly lower when graminoids were removed, whilst PMO was highest in the absence of both vascular PFTs (graminoids and ericoids), but only in the hummocks. 4. Path analyses demonstrate that different plant–soil interactions drive PMP and PMO in peatlands and that changes in biotic and abiotic factors can have auto-amplifying effects on current CH4 dynamics. 5. Synthesis. Changing environmental conditions will, both directly and indirectly, affect peatland processes, causing unforeseen changes in CH4 dynamics. The resilience of peatland CH4 dynamics to environmental change therefore depends on the interaction between plant community composition and microbial communities.

Abstract High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalising syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterise taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth “CS”) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from the survey metadata. Specifically, we modelled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on putative landscape scale pH-abundance responses. We identify that most of the soil OTUs examined exhibit predictable abundance responses across soil pH gradients, though with the exception of known acidophilic lineages, the pH optima of OTU relative abundance was variable and could not be generalised by broad taxonomy. This highlights the need for tools and databases to predict ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER), and as a DADA2 database for use in bioinformatics pipelines. The further development of advanced informatics infrastructures incorporating modelled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios. Competing Interest Statement The authors have declared no competing interest. Footnotes * Updated author details. * https://shiny-apps.ceh.ac.uk/ID-TaxER/ * https://github.com/brijon/ID-TaxER-flat-files

Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes highlighting smaller stoichiometric constraints on community metabolism in examined soils.