Conservation agriculture improves soil health and sustains crop yields after long-term warming.

Climate warming threatens global food security by exacerbating pressures on degraded soils under intensive crop production. Conservation agriculture is promoted as a sustainable solution that improves soil health and sustains crop yields in a changing climate, but these benefits may be affected by long-term warming. Here, we investigate the effects of conservation agriculture compared to conventional agriculture on 17 soil properties, microbial diversity and crop yields, during eight-years' experimental warming. An overall positive effect of warming on soil health over time under conservation agriculture is characterized by linear increases in soil organic carbon and microbial biomass carbon. Warming-triggered shifts in microbial biomass carbon and fungal diversity (saprogen richness) are directly linked to a 9.3% increase in wheat yields over eight years, but only under conservation agriculture. Overall, conservation agriculture results in an average 21% increase in soil health and supports similar levels of crop production after long-term warming compared to conventional agriculture. Our work provides insights into the potential benefits of conservation agriculture for long-term sustainable food production because improved soil health improves resilience to the effects of climate warming.

Extreme rainfall events eliminate the response of greenhouse gas fluxes to hydrological alterations and fertilization in a riparian ecosystem.

Riparian ecosystems are essential carbon dioxide (CO2) sources, which considerably promotes climate warming. However, the other greenhouse gas fluxes (GHGs), such as methane (CH4) and nitrous oxide (N2O), in the riparian ecosystems have not been well studied, and it remains unclear whether and how these GHG fluxes respond to extreme weather, fertilization and hydrological alterations associated with reservoir management. Here, we assessed the impacts of hydrological alterations (i.e., flooding frequency) and fertilization (nitrogen and/or phosphorus) induced by human activities (hydroengineering construction and agricultural activities) on GHG fluxes, and further investigated the underlying mechanisms in two contrasting years (normal vs. extreme rainfall years) in a reservoir riparian zone dominated by grasses. The significant combined effects of extreme rainfall events and human activities (hydrological alterations and fertilization) on the GHGs were observed. Continuous flooding reduced CO2 emissions by 24% but increased CH4 emissions by ∼4 times in a normal rainfall year. In addition, nitrogen fertilization promoted CO2 emissions by 37%. However, these phenomena were not observed in the year with extreme rainfall events, which made the flooding levels homogeneous across the treatments. Furthermore, we found that CO2 fluxes were driven by the soil moisture, nutrient content, aboveground biomass, and root carbon content, while CH4 and N2O fluxes were merely driven by the soil properties (pH, moisture, and nutrient content). This study provides valuable insights into the crucial role of extreme rainfall events, hydrological alteration, and fertilization in regulating GHG fluxes in riparian ecosystems, as well as supports the integration of these changes in GHG emission models.

Aridity drives the response of soil total and particulate organic carbon to drought in temperate grasslands and shrublands.

The increasing prevalence of drought events in grasslands and shrublands worldwide potentially has impacts on soil organic carbon (SOC). We leveraged the International Drought Experiment to study how SOC, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) concentrations, responds to extreme drought treatments (1-in-100-year) for 1 to 5 years at 19 sites worldwide. In more mesic areas (aridity index > 0.65), SOC and POC concentrations decreased by 7.9% (±3.9) and 15.9% (±6.2) with drought, respectively, but there were no impacts on MAOC concentrations. However, drought had no impact on SOC, POC, or MAOC concentrations in drylands (aridity index < 0.65). The response of SOC to drought varied along an aridity gradient, concomitant with interannual precipitation variability and standing SOC concentration gradients. These findings highlight the differing response magnitudes of POC and MAOC concentrations to drought and the key regulating role of aridity.

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.

Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.

Environmental microbiome, human fungal pathogens, and antimicrobial resistance.

Traditionally, antifungal resistance (AFR) has received much less attention compared with bacterial resistance to antibiotics. However, global changes, pandemics, and emerging new fungal infections have highlighted global health consequences of AFR. The recent report of the World Health Organisation (WHO) has identified fungal priority pathogens, and recognised AFR among the greatest global health threats. This is particularly important given the significant increase in fungal infections linked to climate change and pandemics. Environmental factors play critical roles in AFR and fungal infections, as many clinically relevant fungal pathogens and AFR originate from the environment (mainly soil). In addition, the environment serves as a potential rich source for the discovery of new antifungal agents, including mycoviruses and bacterial probiotics, which hold promise for effective therapies. In this article, we summarise the environmental pathways of AFR development and spread among high priority fungal pathogens, and propose potential mechanisms of AFR development and spread. We identify a research priority list to address key knowledge gaps in our understanding of environmental AFR. Further, we propose an integrated roadmap for predictive risk management of AFR that is critical for effective surveillance and forecasting of public health outcomes under current and future climatic conditions.

Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments.

The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally.

Positive soil priming effects are the rule at a global scale.

Priming effects of soil organic matter decomposition are critical to determine carbon budget and turnover in soil. Yet, the overall direction and intensity of soil priming remains under debate. A second-order meta-analysis was performed with 9296-paired observations from 363 primary studies to determine the intensity and general direction of priming effects depending on the compound type, nutrient availability, and ecosystem type. We found that fresh carbon inputs induced positive priming effects (+37%) in 97% of paired observations. Labile compounds induced larger priming effects (+73%) than complex organic compounds (+33%). Nutrients (e.g., N, P) added with organic compounds reduced the intensity of priming effects compared to compounds without N and P, reflecting "nutrient mining from soil organic matter" as one of the main mechanisms of priming effects. Notably, tundra, lakebeds, wetlands, and volcanic soils showed much larger priming effects (+125%) compared to soils under forests, croplands, and grasslands (+24…+32%). Our findings highlight that positive priming effects are predominant in most soils at a global scale. Optimizing strategies to incorporate fresh organic matter and nutrients is urgently needed to offset the priming-induced accelerated organic carbon turnover and possible losses.

Plant species and associated root nutritional traits influence soil dominant bacteria in coastal wetlands across China.

Climate and edaphic properties drive the biogeographic distribution of dominant soil microbial phylotypes in terrestrial ecosystems. However, the impact of plant species and their root nutritional traits on microbial distribution in coastal wetlands remains unclear. Here, we investigated the nutritional traits of 100 halophyte root samples and the bacterial communities in the corresponding soil samples from coastal wetlands across eastern China. This study spans 22° of latitude, covering over 2500 km from north to south. We found that 1% of soil bacterial phylotypes accounted for nearly 30% of the soil bacterial community abundance, suggesting that a few bacterial phylotypes dominated the coastal wetlands. These dominated phylotypes could be grouped into three ecological clusters as per their preference over climatic (temperature and precipitation), edaphic (soil carbon and nitrogen), and plant factors (halophyte vegetation, root carbon, and nitrogen). We further provide novel evidence that plant root nutritional traits, especially root C and N, can strongly influence the distribution of these ecological clusters. Taken together, our study provides solid evidence of revealing the dominance of specific bacterial phylotypes and the complex interactions with their environment, highlighting the importance of plant root nutritional traits on biogeographic distribution of soil microbiome in coastal wetland ecosystems.

Soil health is associated with higher primary productivity across Europe.

Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

Unforeseen plant phenotypic diversity in a dry and grazed world.

Earth harbours an extraordinary plant phenotypic diversity1 that is at risk from ongoing global changes2,3. However, it remains unknown how increasing aridity and livestock grazing pressure-two major drivers of global change4-6-shape the trait covariation that underlies plant phenotypic diversity1,7. Here we assessed how covariation among 20 chemical and morphological traits responds to aridity and grazing pressure within global drylands. Our analysis involved 133,769 trait measurements spanning 1,347 observations of 301 perennial plant species surveyed across 326 plots from 6 continents. Crossing an aridity threshold of approximately 0.7 (close to the transition between semi-arid and arid zones) led to an unexpected 88% increase in trait diversity. This threshold appeared in the presence of grazers, and moved toward lower aridity levels with increasing grazing pressure. Moreover, 57% of observed trait diversity occurred only in the most arid and grazed drylands, highlighting the phenotypic uniqueness of these extreme environments. Our work indicates that drylands act as a global reservoir of plant phenotypic diversity and challenge the pervasive view that harsh environmental conditions reduce plant trait diversity8-10. They also highlight that many alternative strategies may enable plants to cope with increases in environmental stress induced by climate change and land-use intensification.

Major overlap in plant and soil organic carbon hotspots across Africa.

Terrestrial plant and soil organic carbon stocks are critical for regulating climate change, enhancing soil fertility, and supporting biodiversity. While a global-scale decoupling between plant and soil organic carbon has been documented, the hotspots and interconnections between these two carbon compartments across Africa, the second-largest continent on the planet, have been significantly overlooked. Here, we have compiled over 10,000 existing soil organic carbon observations to generate a high-resolution map, illustrating the distribution pattern of soil organic carbon in Africa. We then showed that above- and below-ground plant carbon are significantly and positively correlated with soil organic carbon across Africa. Both soil and plant carbon compartments shared major hotspots in the tropical regions. Our study provides critical insights into the spatial distribution of carbon hotspots across Africa, essential for soil conservation and safeguarding terrestrial carbon stocks amidst the challenges of climate change.

Aboveground and belowground biodiversity have complementary effects on ecosystem functions across global grasslands.

Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.

Unfolding the dynamics of ecosystems undergoing alternating wet-dry transitional states.

A significant fraction of Earth's ecosystems undergoes periodic wet-dry alternating transitional states. These globally distributed water-driven transitional ecosystems, such as intermittent rivers and coastal shorelines, have traditionally been studied as two distinct entities, whereas they constitute a single, interconnected meta-ecosystem. This has resulted in a poor conceptual and empirical understanding of water-driven transitional ecosystems. Here, we develop a conceptual framework that places the temporal availability of water as the core driver of biodiversity and functional patterns of transitional ecosystems at the global scale. Biological covers (e.g., aquatic biofilms and biocrusts) serve as an excellent model system thriving in both aquatic and terrestrial states, where their succession underscores the intricate interplay between these two states. The duration, frequency, and rate of change of wet-dry cycles impose distinct plausible scenarios where different types of biological covers can occur depending on their desiccation/hydration resistance traits. This implies that the distinct eco-evolutionary potential of biological covers, represented by their trait profiles, would support different functions while maintaining similar multifunctionality levels. By embracing multiple alternating transitional states as interconnected entities, our approach can help to better understand and manage global change impacts on biodiversity and multifunctionality in water-driven transitional ecosystems, while providing new avenues for interdisciplinary studies.

Superiority of native soil core microbiomes in supporting plant growth.

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

Fertilization regulates global thresholds in soil bacteria.

Global patterns in soil microbiomes are driven by non-linear environmental thresholds. Fertilization is known to shape the soil microbiome of terrestrial ecosystems worldwide. Yet, whether fertilization influences global thresholds in soil microbiomes remains virtually unknown. Here, utilizing optimized machine learning models with Shapley additive explanations on a dataset of 10,907 soil samples from 24 countries, we discovered that the microbial community response to fertilization is highly dependent on environmental contexts. Furthermore, the interactions among nitrogen (N) addition, pH, and mean annual temperature contribute to non-linear patterns in soil bacterial diversity. Specifically, we observed positive responses within a soil pH range of 5.2-6.6, with the influence of higher temperature (>15°C) on bacterial diversity being positive within this pH range but reversed in more acidic or alkaline soils. Additionally, we revealed the threshold effect of soil organic carbon and total nitrogen, demonstrating how temperature and N addition amount interacted with microbial communities within specific edaphic concentration ranges. Our findings underscore how complex environmental interactions control soil bacterial diversity under fertilization.

Limiting Resources Define the Global Pattern of Soil Microbial Carbon Use Efficiency.

Microbial carbon (C) use efficiency (CUE) delineates the proportion of organic C used by microorganisms for anabolism and ultimately influences the amount of C sequestered in soils. However, the key factors controlling CUE remain enigmatic, leading to considerable uncertainty in understanding soil C retention and predicting its responses to global change factors. Here, we investigate the global patterns of CUE estimate by stoichiometric modeling in surface soils of natural ecosystems, and examine its associations with temperature, precipitation, plant-derived C and soil nutrient availability. We found that CUE is determined by the most limiting resource among these four basic environmental resources within specific climate zones (i.e., tropical, temperate, arid, and cold zones). Higher CUE is common in arid and cold zones and corresponds to limitations in temperature, water, and plant-derived C input, while lower CUE is observed in tropical and temperate zones with widespread limitation of nutrients (e.g., nitrogen or phosphorus) in soil. The contrasting resource limitations among climate zones led to an apparent increase in CUE with increasing latitude. The resource-specific dependence of CUE implies that soils in high latitudes with arid and cold environments may retain less organic C in the future, as warming and increased precipitation can reduce CUE. In contrast, oligotrophic soils in low latitudes may increase organic C retention, as CUE could be increased with concurrent anthropogenic nutrient inputs. The findings underscore the importance of resource limitations for CUE and suggest asymmetric responses of organic C retention in soils across latitudes to global change factors.

The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors.

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.

Thermal sensitivity of soil microbial carbon use efficiency across forest biomes.

Understanding the large-scale pattern of soil microbial carbon use efficiency (CUE) and its temperature sensitivity (CUET) is critical for understanding soil carbon-climate feedback. We used the 18O-H2O tracer method to quantify CUE and CUET along a north-south forest transect. Climate was the primary factor that affected CUE and CUET, predominantly through direct pathways, then by altering soil properties, carbon fractions, microbial structure and functions. Negative CUET (CUE decreases with measuring temperature) in cold forests (mean annual temperature lower than 10 °C) and positive CUET (CUE increases with measuring temperature) in warm forests (mean annual temperature greater than 10 °C) suggest that microbial CUE optimally operates at their adapted temperature. Overall, the plasticity of microbial CUE and its temperature sensitivity alter the feedback of soil carbon to climate warming; that is, a climate-adaptive microbial community has the capacity to reduce carbon loss from soil matrices under corresponding favorable climate conditions.

Intrinsic microbial temperature sensitivity and soil organic carbon decomposition in response to climate change.

Soil microbes are essential for regulating carbon stocks under climate change. However, the uncertainty surrounding how microbial temperature responses control carbon losses under warming conditions highlights a significant gap in our climate change models. To address this issue, we conducted a fine-scale analysis of soil organic carbon composition under different temperature gradients and characterized the corresponding microbial growth and physiology across various paddy soils spanning 4000 km in China. Our results showed that warming altered the composition of organic matter, resulting in a reduction in carbohydrates of approximately 0.026% to 0.030% from humid subtropical regions to humid continental regions. These changes were attributed to a decrease in the proportion of cold-preferring bacteria, leading to significant soil carbon losses. Our findings suggest that intrinsic microbial temperature sensitivity plays a crucial role in determining the rate of soil organic carbon decomposition, providing insights into the temperature limitations faced by microbial activities and their impact on soil carbon-climate feedback.