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In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism–soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.In this Review, Philippot et al. explore how soil microorganisms can affect the physical and chemical properties of soil and discuss the ecological and evolutionary consequences of these microbially driven shifts in soil properties. They also explore how microbially mediated changes in soil properties can be used to combat threats to soil health and other environmental challenges.

Healthy soil is one of the most critical resources for the health and sustainability of ecosystems, including agroecosystems. Although the agroforestry community has long been convinced of the soil health benefits of agroforestry practices, many of such practices remain to be fully accepted by the mainstream agriculture community. Agroforestry, as a sustainable land management practice, has shown solid evidence of its role in improving soil quality and health based on at least four decades of data gathered from the world over. This thematic issue presents 28 papers that add further to the body of knowledge to reaffirm that agroforestry can improve the major measurable soil metrics that define soil health. Collectively, these papers show that agroforestry has the ability to (1) enrich soil organic carbon better than monocropping systems, (2) improve soil nutrient availability and soil fertility due to the presence of trees in the system, and (3) enhance soil microbial dynamics, which would positively influence soil health. It is imperative that agroforestry, as part of a multifunctional land-use strategy, should receive increased attention in our policy discussion for the future of soil and soil health.

AbstractComposting and vermicomposting are sustainable strategies to transform organic wastes into organic amendments, valuable as potting media or soil conditioner. However, the negative aspects of these processes are emissions of greenhouse gases and odorous molecules and final product potentially containing toxic compounds. These negative aspects can be limited through the addition of organic, inorganic or biological additives to the composted or vermicomposted mixture. The aims of this review are (1) to present the main characteristics of composting and vermicomposting processes with and without additives, (2) to show the influence of additives on greenhouse gas emissions during waste degradation and (3) to report the effects of additives on the properties of the final products (heavy metal and nutrient contents), in view of their use as a soil conditioner or potting media. Finally, the feasibility and potential environmental benefits of co-composting and co-vermicomposting are discussed. Our results show that additives affect composting parameters such as temperature, pH and moisture and thus have an impact on the composting process. They may be used to reduce gas emissions and mobility of mineral ions. The various additives have contrasting effects on the quality of the final product and its impact on soil quality. The use of worms and additives seems to increase plant available nutrient contents, while decreasing N leaching, heavy metal mobility and composting time. Co-composting and co-vermicomposting strategies need to be locally optimised, involving the generated amendments in a circular economy to improve sustainability of agricultural systems.

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. Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

Abstract The largest terrestrial organic carbon pool, carbon in soils, is regulated by an intricate connection between plant carbon inputs, microbial activity, and the soil matrix. This is manifested by how microorganisms, the key players in transforming plant-derived carbon into soil organic carbon, are controlled by the physical arrangement of organic and inorganic soil particles. Here we conduct an incubation of isotopically labelled litter to study effects of soil structure on the fate of litter-derived organic matter. While microbial activity and fungal growth is enhanced in the coarser-textured soil, we show that occlusion of organic matter into aggregates and formation of organo-mineral associations occur concurrently on fresh litter surfaces regardless of soil structure. These two mechanisms—the two most prominent processes contributing to the persistence of organic matter—occur directly at plant–soil interfaces, where surfaces of litter constitute a nucleus in the build-up of soil carbon persistence. We extend the notion of plant litter, i.e., particulate organic matter, from solely an easily available and labile carbon substrate, to a functional component at which persistence of soil carbon is directly determined.

Nitrous oxide (N 2 O), like carbon dioxide, is a long-lived greenhouse gas that accumulates in the atmosphere. Over the past 150 years, increasing atmospheric N 2 O concentrations have contributed to stratospheric ozone depletion 1 and climate change 2 , with the current rate of increase estimated at 2 per cent per decade. Existing national inventories do not provide a full picture of N 2 O emissions, owing to their omission of natural sources and limitations in methodology for attributing anthropogenic sources. Here we present a global N 2 O inventory that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control N 2 O emissions. We use bottom-up (inventory, statistical extrapolation of flux measurements, process-based land and ocean modelling) and top-down (atmospheric inversion) approaches to provide a comprehensive quantification of global N 2 O sources and sinks resulting from 21 natural and human sectors between 1980 and 2016. Global N 2 O emissions were 17.0 (minimum–maximum estimates: 12.2–23.5) teragrams of nitrogen per year (bottom-up) and 16.9 (15.9–17.7) teragrams of nitrogen per year (top-down) between 2007 and 2016. Global human-induced emissions, which are dominated by nitrogen additions to croplands, increased by 30% over the past four decades to 7.3 (4.2–11.4) teragrams of nitrogen per year. This increase was mainly responsible for the growth in the atmospheric burden. Our findings point to growing N 2 O emissions in emerging economies—particularly Brazil, China and India. Analysis of process-based model estimates reveals an emerging N 2 O–climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in N 2 O emissions exceeds some of the highest projected emission scenarios 3 , 4 , underscoring the urgency to mitigate N 2 O emissions. Bottom-up and top-down approaches are used to quantify global nitrous oxide sources and sinks resulting from both natural and anthropogenic sources, revealing a 30% increase in global human-induced emissions between 1980 and 2016.

River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.

Lentic systems (lakes and reservoirs) are emission hotpots of nitrous oxide (N2O), a potent greenhouse gas; however, this has not been well quantified yet. Here we examine how multiple environmental forcings have affected N2O emissions from global lentic systems since the pre-industrial period. Our results show that global lentic systems emitted 64.6 ± 12.1 Gg N2O-N yr−1 in the 2010s, increased by 126% since the 1850s. The significance of small lentic systems on mitigating N2O emissions is highlighted due to their substantial emission rates and response to terrestrial environmental changes. Incorporated with riverine emissions, this study indicates that N2O emissions from global inland waters in the 2010s was 319.6 ± 58.2 Gg N yr−1. This suggests a global emission factor of 0.051% for inland water N2O emissions relative to agricultural nitrogen applications and provides the country-level emission factors (ranging from 0 to 0.341%) for improving the methodology for national greenhouse gas emission inventories

Expanding and intensifying agriculture has led to a loss of soil carbon. As agroecosystems cover over 40% of Earth's land surface, they must be part of the solution put in action to mitigate climate change. Development of efficient management practices to maximize soil carbon retention is currently limited, in part, by a poor understanding of how plants, which input carbon to soil, and microbes, which determine its fate there, interact. Here we implement a diversity gradient by intercropping undersown species with barley in a large field trial, ranging from one to eight undersown species. We find that increasing plant diversity strengthens positive associations within the rhizosphere soil microbial community in relation to negative associations. These associations, in turn, enhance community carbon use efficiency. Jointly, our results highlight how increasing plant diversity in agriculture can be used as a management strategy to enhance carbon retention potential in agricultural soils.

Net primary production (NPP) is the foundation of the oceans' ecosystems and the fisheries they support. In the Arctic Ocean, NPP is controlled by a complex interplay of light and nutrients supplied by upwelling as well as lateral inflows from adjacent oceans and land. But so far, the role of the input from land by rivers and coastal erosion has not been given much attention. Here, by upscaling observations from the six largest rivers and using measured coastal erosion rates, we construct a pan-Arctic, spatio-temporally resolved estimate of the land input of carbon and nutrients to the Arctic Ocean. Using an ocean-biogeochemical model, we estimate that this input fuels 28-51% of the current annual Arctic Ocean NPP. This strong enhancement of NPP is a consequence of efficient recycling of the land-derived nutrients on the vast Arctic shelves. Our results thus suggest that nutrient input from the land is a key process that will affect the future evolution of Arctic Ocean NPP.