Quantitative assessment of microbial necromass contribution to soil organic matter

Nitrogen addition decouples the microbial necro-mass from soil organic carbon formation in a temperate grassland

Increasing anthropogenic nitrogen (N) inputs has profoundly altered soil microbial necro-mass carbon (MNC), which serves as a key source of soil organic carbon (SOC). Yet, the response pattern of MNC and its contribution to SOC across a wide range of N addition rates, remain elusive. In a temperate grassland with six years' consecutive N addition spanning seven rates (0-50 g N/(m2·year)) in Inner Mongolia, China, we explored the responses of soil MNC and its contribution to SOC. The soil MNC showed a hump-shaped pattern to increasing N addition rates, with the N saturation threshold at 18.07 g N/(m2·year). The soil MNC was driven by nematode abundance and the ratio of bacterial to fungal biomass below the N threshold, and by plant biomass allocation pattern and diversity above the N threshold. The contribution of soil MNC to SOC declined with increasing N addition rates, and was mainly regulated by the ratio of MNC to mineral-associated organic carbon and plant diversity and the ratio of bacterial to fungal biomass. In addition, the soil MNC and SOC differentially responded to N addition and were mediated by disparate biological and geochemical mechanisms, leading to the decoupled MNC production from SOC formation. Together, in this N-enriched temperate grassland, the soil microbial necro-mass production tends to be insufficient as a general explanation linking SOC formation. This study expands the mechanistic comprehension of the connections between external N input and soil carbon sequestration.

Divergence of microbial carbon use efficiency and soil organic carbon along a tidal flooding gradient in a subtropical coastal wetland

Microbial carbon use efficiency (CUE) typically promotes soil organic carbon (SOC) storage in terrestrial ecosystems. However, this relationship remains poorly understood in coastal wetlands, where tidal flooding creates unique environmental conditions, facilitates lateral transfer and SOC loss, and mediates organic matter exchange between terrestrial and marine systems. Here we examined the CUE-SOC relationship across a tidal flooding gradient (4-25 % frequency) in a subtropical coastal wetland. Along this gradient, SOC decreased by 65 % while microbial CUE increased from 0.24 to 0.32. This inverse relationship coincided with marked compositional shifts: plant debris declined from 57 % to 18 %, while microbial necromass increased from 21 % to 35 %. The enhanced CUE was accompanied by increased turnover times alongside decreased metabolic quotient (qCO2), C-acquiring enzyme activities, soil basal respiration, and microbial biomass carbon (MBC). This enhanced efficiency stemmed from substrate-microbe interactions rather than environmental stresses, as communities transitioned from oligotrophic taxa (α-proteobacteria, Basidiomycota) specializing in recalcitrant terrestrial substrates to copiotrophic microorganisms (γ-proteobacteria, Bacteroidota, Ascomycota) efficiently metabolizing labile marine compounds. Contrary to terrestrial patterns, enhanced CUE did not promote SOC storage due to three key mechanisms: (i) enhanced CUE from marine substrates could not compensate for declining plant debris accumulation; (ii) reduced microbial biomass limited necromass formation despite higher CUE; and (iii) metabolic benefits from high CUE (reduced enzyme activities and respiration rates) could not offset the substantial decrease in SOC inputs. Our findings reveal distinct CUE-SOC relationships in coastal wetlands compared to terrestrial ecosystems, highlighting the importance of considering both terrestrial and marine processes in understanding carbon cycling in these transitional environments.

Changes in long-term land use alter deep soil microbial necromass and organic carbon stabilization

Carbon sequestration in grassland ecosystems plays an important role in alleviating global climate changes. However, the conversion of natural grassland to agricultural cropland has a profound implication for soil organic carbon (OC) sequestration, particularly regarding deep soil carbon stability. Here, we addressed the uncertainties surrounding deep soil OC mineralization by investigating the distribution and stabilization of OC pools in topsoil (0-20 cm) in comparison with that in deep soil (80-100 cm) after 11 and 40 years of agricultural cropland conversion from natural grassland at Hulunbuir, China. It was observed that the conversion substantially reduced the bulk OC in the deep soil, from 44.70 g kg-1 in grassland to 8.76-6.22 g kg-1 in agricultural cropland. Despite this decline, the contribution of mineral-associated OC (MAOC), conversion of microbial necromass C to bulk soil OC, and potential stability of OC increased, indicating a shift towards stabler soil OC forms in agricultural soils. The dissolved organic carbon of the topsoil in the agricultural cropland became more recalcitrant than that in the grassland, while the aliphatic carbon of the MAOC in the deep soil was increased. Although OC mineralization rates were lower in agricultural soils than in the grassland, the temperature sensitivity of OC decomposition (Q10) increased. These findings underscore the importance of assessing soil OC stability under long-term land use changes, with implications for sustainable agricultural management and deep soil carbon's role in climate regulation.

Patterns and controlling factors of soil microbial necromass carbon in global ecosystems

Microbial necromass is a critical source of soil organic carbon (SOC) in terrestrial ecosystems, and the quantity and quality of microbial necromass carbon (MNC) can influence long-term soil carbon sequestration. However, few studies have explored the distribution of soil MNC and its contribution to SOC along the soil profiles across different ecosystems globally. Here, we collected a global dataset (2, 411 samples from 216 papers) of soil MNC at a depth of 0-100 cm depth from wetlands, farmlands, grasslands, and forests. Our findings indicated that the average MNC at 0-30 cm was 2.7 g kg-1 in wetlands, 7.1 g kg-1 in farmlands, 17.2 g kg-1 in grasslands, and 14.6 g kg-1 in forests. The MNC content in deep soils (30-100 cm) was 70 % lower (p < 0.05) than in topsoil (0-30 cm), whereas the contribution of the MNC to the SOC in deep soils (50 %) was higher than in topsoil in forests (32 %). On average, the fungal necromass carbon(FNC) content (7.5 g kg-1) was almost three times higher than the bacterial necromass carbon (BNC) content (2.8 g kg-1) in the topsoill. The mean annual temperature played an important role in affecting the MNC by altering soil total nitrogen, soil texture and microbial biomass. These findings are important for understanding SOC formation mechanisms and the crucial role of microbial necromass in global ecosystems.

Palygorskite enhances microbial necromass carbon accumulation and drives heavy metal immobilization during chicken manure composting

Microbial necromass carbon (MNC) is a critical component of stable organic matter in compost. However, its role in shaping compost microbial communities and influencing heavy metals (HMs), as well as the effect of palygorskite amendment on MNC and HMs, remains unclear. This study investigated MNC accumulation in chicken manure compost, assessed its impact on microbial communities and HM bioavailability, and evaluated the effects of 5 %, 10 %, and 15 % palygorskite additions. Results showed that palygorskite significantly increased the MNC proportion in total organic carbon, with the 15 % palygorskite enhancing 7.2 % compared to CK. This was primarily due to enhanced bacterial necromass carbon (BNC), which contributed 39.6 %-48.6 % of total MNC. Thermal stress and nutrient limitation were key drivers of MNC accumulation. Fungal necromass carbon (FNC), the dominant MNC component, was positively correlated with compost maturity indices. Palygorskite also markedly reduced HM bioavailability, increasing the passivation rates of Cd, Cu, and Zn by 4.3 %-24.4 %, 10.2 %-11.3 %, and 5.4 %-16.1 %, respectively. Structural equation modeling identified palygorskite, MNC, and pH as the main factors controlling HM bioavailability, explaining up to 83 % of the variation. However, the contribution of MNC to HM immobilization declined as palygorskite addition increased. This study clarifies the relationship between microbial necromass and HMs, highlighting the dual role of palygorskite in stabilizing MNC and reducing HM toxicity.

Influence of land management on soil organic matter pools, plant traits and enzymatic activity in mountain grasslands

Mountain grasslands are globally widespread ecosystems which play a pivotal role in several provisioning, regulating, supporting and cultural ecosystem services. Often shaped over centuries by traditional agricultural activities, including mowing and livestock grazing, mountain grasslands are integral to both ecological function and local livelihood. This study investigated the impact of light grazing on the soil-plant system in extensively managed grasslands, with a focus on functional structure and soil-associated ecosystem functions, including soil organic carbon accrual. Five meadows and five pastures were identified in the Central Italian Alps to simulate land-use intensification along an elevational gradient. Both plant compartment and topsoil samples were collected from each site and characterized. Grazed sites showed higher organic carbon, total nitrogen, and available phosphorus contents as well as higher urease activity, resulting in a higher soil organic matter accrual compared to meadows. In contrast, meadows were characterised by higher fluorescein diacetate hydrolase and phosphomonoesterase activities as well as by greater plant biomass and specific leaf area values. The mineral-associated organic matter (MAOM) fraction was the main carbon and nitrogen pool, especially in meadows. Correlations found between MAOM features and plant traits/soil enzymatic activities suggest that MAOM, in both management systems, is not exclusively of microbial origin, but also influenced by the plant component. Finally, particulate organic matter and MAOM showed a different stability both within and between management systems. These findings underscore the importance of a sustainable grassland management in storing organic matter, thus contributing to climate change mitigation, as well as to enhance nutrient cycling and ecosystem health.

Soil microbial necromass carbon contributions to soil organic carbon after three decades of citrus cultivation

Introduction

Citrus is one of the most economically significant fruits globally, and soil organic carbon (SOC) plays a central role in maintaining soil health and fertility. Consequently, enhancing SOC content directly influences both the yield and quality of citrus crops. However, the sources of SOC in citrus orchards and their mechanisms of contribution remains poorly understood.

Methods

This study investigated citrus soils from orchards of varying planting ages by collecting 0-20 cm soil samples. We analyzed amino sugars, glomalin, particulate organic carbon (POC), and mineral-bound organic carbon (MAOC) to examine the source of microbial residue carbon and its contribution to SOC.

Results

The results revealed a significant decrease in microbial residue carbon (MNC), fungal residue carbon (FNC), and bacterial residue carbon (BNC) with increasing orchard age (p < 0.05). Specifically, the MNC in 30-year-old citrus soils was reduced by 46.27% compared to 10-year-old soils, FNC decreased by 45.61%, and BNC by 48.91%. The proportion of microbial residue carbon within SOC significantly decreased as planting years increased (p < 0.05), from 76.82 ± 2.84% in 10-year-old citrus soils to 20.54 ± 4.70% in 30-year-old soils. Furthermore, soil pH, NO₃--N and MAOC were the main factors controlling MNC. MNC showed a significant negative correlation with SOC, indicating a weakened microbial carbon pump function in citrus soils and an increased reliance on other carbon sources, such as plant-derived carbon. Although citrus cultivation had led to a decline in microbial residue carbon over time, it remained a primary source of organic carbon, with its contribution depending on the age of the orchard.

Discussion

These findings offered novel insights into the mechanisms through which intensive citrus cultivation influences microbial necromass contributions to SOC. This study also highlighted the negative impacts of long-term citrus cultivation on soil microbial necromass and offered recommendations for the rehabilitation of aging orchards.

Total nitrogen levels as a key constraint on soil organic carbon stocks across Australian agricultural soils

Understanding how pedoclimatic drivers regulate soil organic carbon (SOC) stock is crucial for gaining insights into terrestrial carbon-climate feedback and thus adaptation to climate change. However, current data-driven SOC predictive models often neglect to incorporate total nitrogen (TN) data, thereby constraining our understanding of carbon-nitrogen interactions and their influences on SOC storage mechanisms across large scales. Utilizing an interpretable machine learning technique, we investigated how key drivers (TN, climate, elevation, land use, pH, SiO2) affect SOC stocks at different soil depths across Australian major agricultural production regions. Incorporating TN into data-based SOC predictive models enhanced the explained variation by approximately 11 %. TN was identified as the predominant factor influencing SOC stocks, accounting for over 47 % of observed variability across all depths and outweighing climate effects in subsurface soils. Furthermore, we identified depth-specific thresholds of TN levels that constrain SOC accumulation: 1.45 mg/g soil for 0-10 cm, 0.80 mg/g soil for 10-20 cm and 0.63 mg/g soil for 20-30 cm. Projections of SOC stocks under different scenarios suggest that achieving these TN thresholds can promote SOC accumulation and help offset SOC losses associated with a 1 °C increase in mean annual temperature. This study underscores TN levels as a key constraint on SOC stocks across Australian agricultural soils, and thus should be explicitly considered when predicting large-scale SOC dynamics and formulating soil carbon sequestration strategies.

Effects of vegetation restoration on soil microbial necromass carbon and organic carbon in grazed and degraded sandy land

Vegetation restoration effectively enhances carbon (C) sequestration and supports the sustainable management of degraded ecosystems. However, its impact on the accumulation of microbial necromass C (NC) and soil organic C (SOC) in degraded and grazed sandy land remains unclear. This study evaluated six restoration types-grazing plot (control), grassland, scrubland, and forestland of Populus alba, Pinus tabuliformis, and Robinia pseudoacacia-to analyze microbial NC and SOC accumulation and identify the factors influencing these changes from the perspectives of soil nutrients, microbial structure, diversity, and activity. Compared with the grazing plot, SOC, bacterial NC, fungal NC, and microbial NC in restored sandy land increased by 64.2-140.9 %, 74.1-101.1 %, 135.7-221.4 %, and 41.5-63.8 %, respectively. The fungal NC:bacterial NC ratio was higher in restored land than in degraded land. Grassland exhibited a higher SOC content than Pinus tabuliformis and Robinia pseudoacacia, while Populus alba showed higher fungal and microbial NC contents than Robinia pseudoacacia. Soil total nitrogen (TN) and β-D-cellobiosidase were identified as key factors influencing SOC and microbial NC accumulation.This study highlights the critical role of vegetation restoration in enhancing soil C sequestration and promoting ecosystem sustainability. These findings provide a theoretical reference for ecological restoration and the sustainable development of degraded sandy land in regional desert steppe ecosystems.

Microbial Immobilization Shapes the Non-Linear Response of Allochthonous Nitrogen Retention to Grassland Acidification Within Soil Aggregates

Soil nitrogen (N) retention plays a crucial role in determining the ecosystem capacity to buffer anthropogenic N inputs and provides a sustainable N supply. However, the effect of acidification, driven by atmospheric deposition of N and sulfur (S), on the retention and fate of allochthonous N across soil aggregate size classes remains poorly understood. We utilized a soil-acidification gradient induced by 0-50 g S m-2 year-1 addition to investigate 15N recovery in soil N pools within aggregates 21 days after labeling in a Eurasian meadow. Macroaggregates showed higher 15N recovery in microbial biomass, amino acids, amino sugars, and therefore total N (TN), as well as greater sensitivity of the former two fractions to acidification compared to microaggregates. This was accompanied by higher N hydrolases and net N mineralization in macroaggregates, supporting the aggregate hierarchical theory. Under moderate acidification (pH decrease from 7 to 6), 15N retention in hydrolyzable ammonium, amino sugars, non-hydrolyzable N, and TN decreased, likely due to lower microbial immobilization and entombing of allochthonous N. Conversely, severe acidification (pH decrease below 6) enhanced 15N retention in these N fractions through stabilization of microbial necromass, revealing a non-linear relationship between acidification and 15N retention. Concentrations of autochthonous organic N fractions remained unchanged after five-year acidification. These findings underscore the mediating role of soil microbes across aggregates in allochthonous 15N retention among N fractions with contrasting bioavailability under acidification.

Soil Carbon Saturation: What Do We Really Know?

Managing soils to increase organic carbon storage presents a potential opportunity to mitigate and adapt to global change challenges, while providing numerous co-benefits and ecosystem services. However, soils differ widely in their potential for carbon sequestration, and knowledge of biophysical limits to carbon accumulation may aid in informing priority regions. Consequently, there is great interest in assessing whether soils exhibit a maximum capacity for storing organic carbon, particularly within organo-mineral associations given the finite nature of reactive minerals in a soil. While the concept of soil carbon saturation has existed for over 25 years, recent studies have argued for and against its importance. Here, we summarize the conceptual understanding of soil carbon saturation at both micro- and macro-scales, define key terminology, and address common concerns and misconceptions. We review methods used to quantify soil carbon saturation, highlighting the theory and potential caveats of each approach. Critically, we explore the utility of the principles of soil carbon saturation for informing carbon accumulation, vulnerability to loss, and representations in process-based models. We highlight key knowledge gaps and propose next steps for furthering our mechanistic understanding of soil carbon saturation and its implications for soil management.

Cereal-legume intercropping stimulates straw decomposition and promotes soil organic carbon stability

Increasing carbon (C) sequestration and stability in agricultural soils is a key strategy to mitigate climate change towards C neutrality. Crop diversification is an initiative to increase C sequestration in fields, but it is unclear how legume-based crop diversification impacts the functional components of soil organic carbon (SOC) in dryland, including the formation and transformation of particulate organic carbon (POC) and mineral-associated organic carbon (MAOC). We investigated the decomposition of straw residues, the fate of photosynthesized C, as well as the formation of MAOC and POC fractions using an in situ13C labeling technique in the soybean-wheat intercropping, soybean-maize intercropping and their respective monocropping systems, with and without cover crops. After 4-year treatments, the total SOC content in bulk soil remained unchanged, while MAOC content increased significantly by 5.6% with intercropping. Moreover, the in situ13C labeling results confirmed that more photosynthesized C was transferred to MAOC, and less was retained in the POC fraction. Intercropping significantly increased total soil N and mineral N content by 15.3% and 13.4%, respectively, and decreased soil and microbial C/N ratio by 11.3% and 17.4%, respectively. This outcome, therefore, relieved microbial N limitation and accelerated straw residue decomposition. Accordingly, the potential of MAOC formation was strengthened for better SOC persistence. Our study suggests that legume-based crop diversification can effectively enrich N and support POC transformation to MAOC, accordingly contributing to the persistent SOC pool and thus potentially achieving C neutrality under climate change in dryland agroecosystems.

Belowground energy fluxes determine tree diversity effects on above- and belowground food webs

Worldwide tree diversity loss raises concerns about functional and energetic declines across trophic levels. In this study, we coupled 160 above- and belowground food webs, quantifying energy fluxes to microorganisms and invertebrates in a tree-mycorrhiza diversity experiment, to test how tree diversity affects fluxes of energy above and below the ground. The experiment differentiates three mycorrhizal type treatments: only AM tree species (with arbuscular mycorrhizae), only EcM tree species (with ectomycorrhizae; one, two, and four tree species), or mixtures of both AM and EcM tree species (AM+EcM; two and four tree species). Our results indicate that most energy initially flowed through belowground communities, with soil microorganisms contributing 97.7% of total energy and belowground fauna accounting for 60.9% of energy to animals. Consequently, belowground fauna fueled surface (62.3% of predation) and aboveground (30.5% of predation) predators. Tree diversity increased ecosystem multifunctionality (indicated by total and averaged energy fluxes) by ∼30% and energy across most trophic levels in EcM tree communities, while it shifted food webs from fast (such as bacterial-dominated) to slow (such as fungal-dominated) channels in AM tree communities. Tree diversity primarily impacted energy fluxes through belowground communities and strengthened the coupling of above- and belowground food webs, with increasing importance of belowground prey for predators at the soil surface and above the ground. These findings highlight that tree diversity and mycorrhizal types drive above- and belowground ecosystem functioning via belowground energy fluxes.

Fungal endophytes influence soil organic carbon and nitrogen fractions promoting carbon sequestration and improving grain yield in soybean

Fungal endophyte inoculants present a promising avenue for enhancing carbon sequestration in agricultural systems. These endophytes can significantly influence soil organic carbon (SOC) and nitrogen (N) fractions by modulating root exudation, soil aggregation, and organic matter decomposition. We investigated the effectiveness of commercial-stage fungal endophyte seed inoculants in an Australian soybean field trial to increase yield, total SOC, stable SOC fractions, and soil N. After one growing season, specific inoculants (Thozetella sp. and Leptodontidium sp.) and dosages increased soybean grain yield and stocks of soil organic matter (SOM) as aggregate occluded particulate organic matter (oPOM) C and N, and mineral-associated organic matter (MAOM) C and N in the topsoil layer (0-15 cm). Furthermore, positive correlations were established between grain yield and the stocks of oPOM (C and N) and MAOM (C and N) in the topsoil layer (0-15 cm). Importantly, increasing grain yield was significantly and positively associated with the proportion of oPOM-C and N stocks to total SOM stock, providing evidence of significant carbon sequestration in oPOM. However, the proportion of MAOM-C and N stock to total SOM stock decreased significantly with increasing grain yield, indicating higher proportion of MAOM is being turned over relative to other SOM fractions although the absolute amounts of MAOM-C and N remained stable. These findings suggest that fungal endophytes and dosages may have variable but potentially beneficial impacts on crop growth, yield and play a crucial role in altering SOM fractions. This alteration potentially leads to changed carbon sequestration strategies, emphasising the need for further research into fungal endophyte-mediated carbon sequestration mechanisms.

Reapplication of glyphosate mitigate fitness costs for soil bacterial communities

Glyphosate (GLP) is a globally ubiquitous herbicide that poses a threat to living organisms due to its widespread presence in soil ecosystems. However, the results of current research regarding the effects of glyphosate on soil microorganisms and its ecological risks are vague and inconsistent. In this study, we investigated the impact of single (low/high-dose) and reapplication (high-dose) of glyphosate applications on soil microbes through indoor incubation experiments using 16S rRNA gene high-throughput sequencing technology. Our findings indicate that in the short term, whether it's single or reapplication glyphosate applications, changes in diversities of soil bacterial community were less than those in community composition. Glyphosate exerts selective pressure on soil microbial communities, resulting in a predominant process of species replacement after glyphosate application, and quantitative analysis revealed a higher turnover rate of microbial communities under glyphosate reapplication. Factors related to nitrogen cycling, especially NH4+-N and NO3--N, were identified as the main drivers responsible for the changes in soil microbial community composition following glyphosate addition. Changes in the functionality of soil microbial communities are observed after glyphosate application, with the adaptability of microbial communities resulting in smaller changes with reapplication addition compared to a single application. Furthermore, We observed that glyphosate application leads to a phenomenon resembling the "fitness cost" found in resistant bacteria. When glyphosate as a single application, it has a significant impact on bacterial communities, leading to decreased community diversity, stability, and function, alongside alterations in community structure, however, the effect can be mitigated by reapplying glyphosate.

Differential contributions of microbial necromass to humic acid during composting of organic wastes

Microbial necromass is a crucial source of stable organic matter in composting, yet its role in the humification process remains poorly understood. This study aims to explore the contribution of microbial necromass carbon (MNC) to humic acid (HA) formation during the composting of sewage sludge (SS), kitchen waste (KW), and pig manure (PM), and to examine the involvement of fungal communities in microbial necromass humification. The results show that fungal necromass carbon (FNC) consistently contributes more to MNC than bacterial necromass carbon (BNC), with FNC accounting for over 60% of MNC across all treatments. KW exhibited the highest accumulation of FNC (4.09-98.92 g/kg), and its MNC contribution to total organic carbon was 23.63%, significantly higher than sewage sludge (5.57%) and pig manure (7.47%). The carbon-to-nitrogen (C/N) ratio was found to be a critical factor influencing microbial growth, necromass accumulation, and HA formation, with a lower C/N ratio promoting faster microbial turnover and enhancing MNC contribution to HA. The analysis also revealed that Ascomycota dominated the maturation phase, with a significant role in driving humification, especially in KW. Structural equation modeling confirmed that FNC and BNC are directly influenced by the C/N ratio, which in turn affects HA formation This study enhances our understanding of microbial necromass dynamics and its contribution to humic substance formation, providing valuable insights for improving compost quality and optimizing composting strategies for enhanced carbon sequestration.

Soil Bacterial Community Characteristics and Functional Analysis of Estuarine Wetlands and Nearshore Estuarine Wetlands in Qinghai Lake

Qinghai Lake, the largest inland saline lake in China, plays a vital role in wetland carbon cycling. However, the structure and function of soil bacterial communities in its estuarine and nearshore estuarine wetlands remain unclear. This study examined the effects of wetland type and soil depth on bacterial diversity, community composition, and functional potential in the Shaliu, Heima, and Daotang River wetlands using high-throughput sequencing. The results showed that wetland type and soil depth significantly influenced bacterial communities. Nearshore wetlands exhibited lower bacterial diversity in the 0-10 cm layer, while deeper soils (10-20 cm) showed greater regional differentiation. Estuarine wetlands were enriched with Proteobacteria, Actinobacteriota, and Chloroflexi, whereas nearshore wetlands were dominated by Actinobacteriota and Cyanobacteria. Functionally, estuarine wetlands had higher sulfate reduction and anaerobic decomposition potential, with Desulfovibrio, Desulfobacter, and Desulfotomaculum regulating sulfur cycling and carbon decomposition. In contrast, nearshore wetlands showed greater nitrogen fixation and organic matter degradation, facilitated by Rhizobium, Azotobacter, Clostridium, and nitrogen-fixing Cyanobacteria (e.g., Anabaena, Nostoc). Microbial metabolic functions varied by depth: surface soils (0-10 cm) favored environmental adaptation and organic degradation, whereas deeper soils (10-20 cm) exhibited lipid metabolism and DNA repair strategies for low-oxygen adaptation. These findings highlight the spatial heterogeneity of bacterial communities and their role in biogeochemical cycles, providing insights into wetland carbon dynamics and informing conservation strategies.

Soil organic carbon thresholds control fertilizer effects on carbon accrual in croplands worldwide

Initiatives to restore soil fertility and mitigate global warming rely on rebuilding soil organic carbon (SOC). Nitrogen (N) fertilization is crucial for crop yields but affects SOC unpredictably due to varying responses of particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) pools to initial SOC levels. To clarify these effects, here, by combining a global meta-analysis with continental-scale field experiments, we determine that an initial SOC threshold of 15 g C kg-1 controls the effect of N fertilization on POC and MAOC. In SOC-poor soils (< 15 g C kg-1), N fertilizer increases plant-derived C inputs and promotes soil aggregation, favouring POC accumulation. Conversely, in SOC-rich soils, N fertilizer stimulates microbial metabolic efficiency, leading to larger necromass production and stabilization by mineral protection, observed as more pronounced MAOC accrual. Our findings reveal how SOC thresholds shape the response of active and stable carbon pools to N fertilization, with consequences for SOC accrual in cropland soils globally.

Exploring the plant microbiome: A pathway to climate-smart crops

The advent of semi-dwarf crop varieties and fertilizers during the Green Revolution boosted yields and food security. However, unintended consequences such as environmental pollution and greenhouse gas emissions underscore the need for strategies to mitigate these impacts. Manipulating rhizosphere microbiomes, an aspect overlooked during crop domestication, offers a pathway for sustainable agriculture. We propose that modulating plant microbiomes can help establish "climate-smart crops" that improve yield and reduce negative impacts on the environment. Our proposed framework integrates plant genotype, root exudates, and microbes to optimize nutrient cycling, improve stress resilience, and expedite carbon sequestration. Integrating unselected ecological traits into crop breeding can promote agricultural sustainability, illuminating the nexus between plant genetics and ecosystem functioning.

Decreased stability of soil dissolved organic matter under disturbance of periodic flooding and drying in reservoir drawdown area

Dissolved organic matter (DOM) constitutes the largest active carbon pool on earth, playing a crucial role in numerous biogeochemical processes. Understanding the molecular characteristics and chemical properties of DOM is essential for comprehending the global carbon cycle. However, there is a lack of systematic understanding regarding the influence of periodic flooding and drying, caused by reservoir operations, on the sources, characteristics and stability of soil DOM in the drawdown area, as well as the biotic and abiotic processes regulating DOM changes. This study employs Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and 16S rRNA sequencing to investigate the variations in molecular and compound composition of soil DOM at different elevations in the drawdown area of the Three Gorges Reservoir, and their associations with microbial communities. The results indicate that with the increasing duration of flooding, the proportion of easily degradable DOM gradually increases in the drawdown area soils, while the proportion of refractory DOM decreases. Periodic flooding and drying enhance the microbial authigenic components of DOM, reduce the plant-derived DOM components, and significantly decrease the stability, aromaticity, and unsaturation of soil DOM. Soil DOM engages in the biogeochemical processes of the drawdown area ecosystem through coupled changes with bacteria and archaea, and changes in soil DOM result in variations in microbial necromass carbon and lignin phenol content at different elevations. The findings are significant for deepening the understanding of the biogeochemical processes involving soil DOM in drawdown areas.

Differential responses of plant and microbial respiration to extreme precipitation and drought during spring and summer in the Eurasian meadow steppe

Increasing extreme precipitation and drought events along changes in their seasonal patterns due to climate change are expected to have profound consequences for carbon cycling. However, how these climate extremes impact ecosystem respiration (Reco) and whether these impacts differ between seasons remain unclear. Here, we reveal the responses of Reco and its components to extreme precipitation and drought in spring and summer by conducting a five-year manipulative experiment in a temperate meadow steppe. Based on a 5-year average, the seasonal mean values (±SE) of Reco, Rh, Rroot, Rabg and Rplant significantly increased (p < 0.01) under both extreme precipitation treatments: wet spring (WSP) and wet summer (WSU), and significantly decreased (p < 0.01) under both extreme drought treatments: dry spring (DSP) and dry summer (DSU), except in Rabg under DSU, which remained comparable to the control. The sensitivity of Reco, Rh, Rroot and Rplant to extreme precipitation was significantly higher in spring than in summer. On average, Rplant was the primary contributor of Reco, accounting for 37.18% and 38.31% of the total across all its components under WSP and WSU, respectively during the growing season over the five study years. Moreover, linear models revealed Rplant explained 87% of the variance in Reco. Our findings indicate that future changes in precipitation events, particularly extreme precipitation may lead to increased carbon release from ecosystems, largely driven by enhanced plant respiration rather than microbial respiration. However, due to this study focused solely on respiration and did not measure photosynthesis, the findings represent only the carbon release processes and do not account for potential carbon uptake by plants during the same conditions. These emergent identified contribution to ecosystem respiration provide valuable insights for improving model benchmarks to better predict ecosystem respiration responses to extreme climate in specified season.

Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis

Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3--N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.

Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes

Soil microbial communities play crucial roles in nutrient cycling and can help retain nitrogen in agricultural soils. Quantitative stable isotope probing (qSIP) is a useful method for investigating taxon-specific microbial growth and utilization of specific nutrients, such as nitrogen (N). Typically, qSIP is performed in a highly controlled lab setting, so the field relevance of lab qSIP studies remains unknown. We conducted and compared tandem lab and field qSIP to quantify the assimilation of 15N by maize-associated soil prokaryotic communities at two agricultural sites. Here, we show that field qSIP with 15N can be used to measure taxon-specific microbial N assimilation. Relative 15N assimilation rates were generally lower in the field, and the magnitude of this difference varied by site. Rates differed by method (lab vs field) for 19% of the top N assimilating genera. The field and lab measures were more comparable when relative assimilation rates were weighted by relative abundance to estimate the proportion of N assimilated by each genus with only ~10% of taxa differing by method. Of those that differed, the taxa consistently higher in the lab were inclined to have opportunistic lifestyle strategies, whereas those higher in the field had niches reliant on plant roots or in-tact soil structure (biofilms, mycelia). This study demonstrates that 15N-qSIP can be successfully performed using field-incubated soils to identify microbial allies in N retention and highlights the strengths and limitations of field and lab qSIP approaches.

IMPORTANCE

Soil microbes are responsible for critical biogeochemical processes in natural and agricultural ecosystems. Despite their importance, the functional traits of most soil organisms remain woefully under-characterized, limiting our ability to understand how microbial populations influence the transformation of elements such as nitrogen (N) in soil. Quantitative stable isotope probing (qSIP) is a powerful tool to measure the traits of individual taxa. This method has rarely been applied in the field or with 15N to measure nitrogen assimilation. In this study, we measured genus-specific microbial nitrogen assimilation in two agricultural soils and compared field and lab 15N qSIP methods. Our results identify taxa important for nitrogen assimilation in agricultural soils, shed light on the field relevance of lab qSIP studies, and provide guidance for the future application of qSIP to measure microbial traits in the field.

Mycorrhiza increases plant diversity and soil carbon storage in grasslands

Experimental studies have shown that symbiotic relationships between arbuscular mycorrhizal (AM) fungi and host plants can regulate soil organic carbon (SOC) storage. Although the impacts of mycorrhiza are highly context-dependent, it remains unclear how these effects vary across broad spatial scales. Based on data from 2296 field sites across grassland ecosystems of China, here we show that mycorrhizal fungi symbiosis enhances SOC storage in the topsoil and subsoil through increasing plant diversity and elevating biomass allocation to belowground. SOC storage is significantly higher in both the topsoil and subsoil in systems dominated by obligate mycorrhizal (OM) and facultative mycorrhizal (FM) plants than those dominated by nonmycorrhizal (NM) plants. Also, the relative abundance of OM plants increases at the expense of FM plants as temperature and precipitation increase. These findings provide valuable insights into the potential mechanisms by which mycorrhizal fungi may influence grassland plant diversity and SOC storage in the context of global change.

Thinning Intensity Enhances Soil Multifunctionality and Microbial Residue Contributions to Organic Carbon Sequestration in Chinese Fir Plantations

Soil multifunctionality is essential for the enhancement of soil carbon sequestration, but disturbances such as thinning practices can influence soil microbial activity and carbon cycling. Microbial residues, particularly microbial residue carbon (MRC), are important contributors to soil organic carbon (SOC), but the effects of thinning intensity on MRC accumulation remain poorly understood. This study evaluated the impact of four thinning treatments-control (CK, 0%), light-intensity thinning (LIT, 20%), medium-intensity thinning (MIT, 30%), and high-intensity thinning (HIT, 45%)-on soil multifunctionality in Chinese fir plantations five years after thinning. Soil nutrient provision, microbial biomass, enzyme activity, and microbial residue carbon were assessed. The results showed that thinning intensity significantly affected soil nutrient provision and microbial biomass, with MIT and HIT showing higher nutrient levels than CK and LIT. Specifically, MIT's and HIT's total nutrient provision increased by 0.04 and 0.15 compared to that of CK. Enzyme activity was highest in LIT (+0.89), followed by MIT (+0.07), with HIT showing a decline (-0.84). Microbial biomass, including bacterial PLFAs (B-PLFAs), fungal PLFAs (F-PLFAs), microbial biomass carbon (MBC), and nitrogen (MBN), was highest in CK and MIT, and lowest in HIT, with MIT showing a 0.13 increase compared to CK. Microbial residue carbon (MRC) accumulation was positively correlated with soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), and easily oxidized organic carbon (EOC). The highest MRC content in the 0-20 cm soil layer was observed in MIT and CK (10.46 and 11.66 g/kg, respectively), while the MRC in LIT and HIT was significantly lower, reduced by 24% and 12%, respectively. These findings highlight the significant role of thinning intensity in microbial activity and carbon cycling. Medium-intensity thinning (MIT, 30%) was identified as the most effective approach for promoting microbial biomass and enhancing carbon cycling in Chinese fir forest soils, making it an optimal approach for forest management aimed at increasing soil carbon sequestration.

Decoupled responses of soil microbial diversity and ecosystem functions to successive degeneration processes in alpine pioneer community

Many alpine ecosystems are undergoing vegetation degradation because of global changes, which are affecting ecosystem functioning and biodiversity. The ecological consequences of alpine pioneer community degradation have been less studied than glacial retreat or meadow degradation in alpine ecosystems. We document the comprehensive responses of microbial community characteristics to degradation processes using field-based sampling, conduct soil microcosm experiments to simulate the effects of global change on microorganisms, and explore their relationships to ecosystem functioning across stages of alpine pioneer community degradation. Our work provides the first evidence that alpine pioneer community degradation led to declines of 27% in fungal richness, 8% in bacterial richness, and about 50% in endemic microorganisms. As vegetation degraded, key ecosystem functions such as nutrient availability, soil enzymatic activity, microbial biomass, and ecosystem multifunctionality progressively increased. However, soil respiration rate and carbon storage exhibited unbalanced dynamics. Respiration rate increased by 190% during the middle stage of degradation compared with the primary stage, and it decreased by 38% in the later stage. This indicates that soil carbon loss or emission increases during the mid-successional stage, whereas in later successional stages, alpine meadows become significant carbon sinks. Compared with microbial community characteristics (such as richness of total and functional taxa, and network complexity), community resistance contributes more significantly to ecosystem functions. Especially, the bacterial community resistance is crucial for ecosystem functioning, yet it is greatly impaired by nitrogen addition. Based on microbial network, community assembly, and community resistance analyses, we conclude that fungi are more vulnerable to environmental changes and show smaller contributions to ecosystem functions than bacteria in degrading alpine ecosystems. Our findings enhance the knowledge of the distinct and synergistic functional contributions of microbial communities in degrading alpine ecosystems and offer guidance for developing restoration strategies that optimize ecosystem functioning of degraded alpine plant communities.

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

Short-term warming supports mineral-associated carbon accrual in abandoned croplands

Effective soil organic carbon (SOC) management can mitigate the impact of climate warming. However, the response of different SOC fractions to warming in abandoned croplands remains unclear. Here, categorizing SOC into particulate and mineral-associated organic carbon (POC and MAOC) with physical fractionation, we investigate the responses of POC and MAOC content and temperature sensitivity (Q10) to warming through a 3-year in situ warming experiment (+1.6 °C) in abandoned croplands across 12 sites in China (latitude: 22.33-46.58°N). Our results indicate that POC content remains unchanged while MAOC content significantly increases under warming. POC and MAOC content changes are mainly influenced by root biomass and microbial necromass carbon changes, respectively. The Q10 of MAOC is significantly lower than that of POC regardless of the warming or control treatment, suggesting that MAOC represents the most persistent and least vulnerable carbon fraction within SOC. Collectively, the sequestration of stable soil carbon can be enhanced in abandoned croplands under short-term warming.

Fungal-mediated soil aggregation as a mechanism for carbon stabilization

Soils can potentially be turned into net carbon sinks for atmospheric carbon to offset anthropogenic greenhouse gas emissions. Occlusion of soil organic carbon in soil aggregates is a key mechanism, which temporarily protects it from decomposition by soil organisms. Filamentous fungi are recognized for their positive role in the formation and stabilization of aggregates. In this review, we assess the current knowledge of the contribution of fungi to soil aggregation and set a new research agenda to quantify fungal-mediated aggregation across different climates and soils. Our review highlights three main knowledge gaps: (1) the lack of quantitative data and mechanistic understanding of aggregate turnover under field conditions, (2) lack of data on the biochemical and biological mechanisms by which filamentous fungi influence soil aggregation, and (3) uncharacterized contribution of soil fungi across environments. Adopting a trait-based approach to increase the level of mechanistic understanding between fungal diversity and soil structure seems promising, but will need additional experiments in which fungal diversity is manipulated by either removal through sieving or dilution, or addition through using synthetic communities of cultured fungi. We stress the importance of integrating ecological and physicochemical perspectives for accurate modelling of soil aggregation and soil organic carbon cycling, which is needed to successfully predict the effects of land management strategies.

Unlocking Mechanisms for Soil Organic Matter Accumulation: Carbon Use Efficiency and Microbial Necromass as the Keys

Soil microorganisms transform plant-derived C (carbon) into particulate organic C (POC) and mineral-associated C (MAOC) pools. While microbial carbon use efficiency (CUE) is widely recognized in current biogeochemical models as a key predictor of soil organic carbon (SOC) storage, large-scale empirical evidence is limited. In this study, we proposed and experimentally tested two predictors of POC and MAOC pool formation: microbial necromass (using amino sugars as a proxy) and CUE (by 18O-H2O approach). Soil sampling (0-10 and 10-20 cm depth) was conducted along a climatic transect of 900 km on the Loess Plateau, including cropland, grassland, shrubland, and forest ecosystems, to ensure the homogeneous soil parent material. We found the highest POC and MAOC accumulation occurred in zones of MAT between 5°C and 10°C or MAP between 300 and 500 mm. Microbial necromass C was more positively related to POC than MAOC (p < 0.05), suggesting that microbial residues may improve POC pool more strongly compared to MAOC pool. Random forest and linear regression analyses showed that POC increased with fungal necromass C, whereas bacterial necromass C drove MAOC. Microbial CUE was coupled with MAOC (p < 0.05) but decoupled with POC and SOC (p > 0.05). The POC have faster turnover rate due to the lack of clay protection, which may lead to the rapid turnover of microbial necromass and thus their decoupling from the CUE. In this sense, the SOC accumulation is driven by microbial necromass, whereas CUE explains MAOC dynamics. Our findings highlight the insufficiency of relying solely on microbial carbon use efficiency (CUE) to predict bulk SOC storage. Instead, we propose that CUE and microbial necromass should be used together to explain SOC dynamics, each influencing distinct C pools.

Changes of bacterial necromass and their roles in humus conversion during organic wastes composting from different sources

This study compared the changes of bacterial necromass carbon (BNC) in composting of three distinct organic wastes [sewage sludge (SW), kitchen waste (KW), and pig manure (PM)] and their relationship with bacterial communities and humus formation. Results revealed that BNC content significantly differed across treatments, with KW exhibiting the highest level at 13 mg/g, followed by PM, where BNC changed between 8 % and 444 % of microbial biomass. Humification index and degree of polymerization indicated that PM had higher humification potential. Network analysis showed that key bacterial phyla contributing to BNC included Firmicutes in KW and Proteobacteria and Gemmatimonadota in SW and PM. Structural equation modeling demonstrated that BNC promoted the formation of humic acid in KW, while core bacteria facilitated the conversion of fulvic acid to humic acid in PM. These findings underscored the crucial role of bacterial necromass in enhancing humification and highlighted the distinct humification processes in composting.

Nitrogen addition promotes soil carbon accumulation globally

Soil is the largest carbon (C) reservoir in terrestrial ecosystems and plays a crucial role in regulating the global C cycle and climate change. Increasing nitrogen (N) deposition has been widely considered as a critical factor affecting soil organic carbon (SOC) storage, but its effect on SOC components with different stability remains unclear. Here, we analyzed extensive empirical data from 304 sites worldwide to investigate how SOC and its components respond to N addition. Our analysis showed that N addition led to a significant increase in bulk SOC (6.7%), with greater increases in croplands (10.6%) and forests (6.0%) compared to grasslands (2.1%). Regarding SOC components, N addition promoted the accumulation of plant-derived C (9.7%-28.5%) over microbial-derived C (0.2%), as well as labile (5.7%) over recalcitrant components (-1.2%), resulting in a shift towards increased accumulation of plant-derived labile C. Consistently, N addition led to a greater increase in particulate organic C (11.9%) than mineral-associated organic C (3.6%), suggesting that N addition promotes C accumulation across all pools, with more increase in unstable than stable pools. The responses of SOC and its components were best predicted by the N addition rate and net primary productivity. Overall, our findings suggest that N enrichment could promote the accumulation of plant-derived and non-mineral associated C and a subsequent decrease in the overall stability of soil C pool, which underscores the importance of considering the effects of N enrichment on SOC components for a better understanding of C dynamics in soils.

Microbial necromass carbon contributed to soil organic carbon accumulation and stabilization in the newly formed inland wetlands

Inland wetlands might be an important "carbon sink", and the chronosequence development of newly formed inland wetlands offers a natural and suitable opportunity for studying the dynamic effect of plant and microbial necromass carbon (PlantC and MNC) on the soil organic carbon (SOC) stabilization. The space-for-time chronosequence approach was used and plots were established in the three ages of newly formed inland wetlands (2, 5, and 16 years). Soil samples were collected in the surface (0-10 cm) and subsurface soil (20-30 cm). Results showed that accumulation of SOC, PlantC, and MNC were significantly larger in the surface than those in the subsurface soil. Moreover, MNC stocks were more abundant than PlantC in the wetland ecosystem both in the surface and subsurface soil. During the chronosequence development, dynamics of SOC and its components accumulation were similar to MNC, both exhibiting an increasing and then decreasing trend in the surface and subsurface soil, except for free particulate organic carbon in the subsurface soil. Structural equation models revealed that changes of MNC affected by environmental variables were the main cause of MAOC dynamics both in the surface and subsurface soil, suggesting that contribution of MNC to MAOC would be the key way of carbon stabilization in the newly formed inland wetlands. Furthermore, MNC accumulation in the surface soil was closely linked to pH, CEC, and soil texture, while in the subsurface soil affected by soil nutrients (TN and NH4+-N). Particularly, despite the decreasing SOC stocks in the 16-year wetland, the stability has significantly enhanced due to the increasing persistent individual amino sugars. This study provides new information on the dynamics of SOC accumulation and highlights the significance of MNC on the SOC sequestration in the newly formed inland wetlands, which is important for the understanding of wetland SOC stock dynamics and stabilization mechanisms.

Long-term nitrogen application decreased mineral-associated organic carbon while increasing particulate organic carbon in purple soil in southwest China

In recent years, anthropogenic activities have increased nitrogen (N) input into terrestrial ecosystems, profoundly impacting soil organic carbon (SOC) sequestration. However, the potential mechanisms through which N affects mineral-associated organic carbon (MAOC) and particulate organic carbon (POC) remain unclear. To address this gap, we conducted a 12-year field trial applying continuous N application (0, 90, 180, 270, and 360 kg N·ha-1) in a maize agro-ecosystem. We assessed plant biomass (yield, straw, and root biomass), microbial properties (enzyme activity, biomass, and diversity), soil chemistry (pH, N availability, and base ions), mineralogy (oxides and silicates), and SOC fractions to elucidate the primary control mechanisms influencing MAOC and POC. Our findings showed that N application increased SOC and POC by 6.56%-10.4% and 43.1%-54.0%, respectively, but decreased MAOC by 7.31%-17.1%. And N application increased plant biomass, but decreased soil pH (pH from 6.7 to 5.6), base ion concentrations (K⁺, Na⁺, Ca2⁺, Mg2⁺), amorphous oxides, and illite content. Partial least squares path model (PLS-PM) and correlation analyses indicated that N application enhances root biomass while increasing microbial decomposition, and ultimately their combined effect increased POC. The decline in MAOC is primarily attributed to soil acidification decreasing the C input from microbial residues, altering mineral composition and diminishing the minerals' capacity to protect SOC. Thus, our study demonstrates that N addition predominantly increases POC through enhanced root biomass, while reducing MAOC by decreasing microbial biomass and weakening mineral protection. These insights provide a deeper understanding of the mechanisms governing SOC fraction dynamics in answer to N inputs in agroecosystems.

Climate, plant and microorganisms jointly influence soil organic matter fractions in temperate grasslands

Soil organic carbon (SOC) plays a critical role in mitigating climate change. Conceptualizing SOC into particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) helps us more accurately predict the responses of organic carbon, with varying chemical composition, molecular size, and degree of association with soil minerals, to environmental changes. To assess the controlling factors of particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), plant and soil samples were collected from 54 temperate grassland sites in Northern China, and the impacts of climate, plants, soil properties and microorganisms on POC and MAOC contents were analyzed. The results indicated that POC slightly dominated temperate grassland topsoils. Climate, plants, and microorganisms could predict a significant portion of the variation in POC and MAOC contents. Microbial factors, represented by fungal and bacterial biomass and necromass carbon, explained 56.6 % and 46.7 % of the variation in POC and MAOC contents, respectively. These findings indicate that the potential of POC in soil carbon storage cannot be ignored, and microorganisms should be considered when studying the dynamics and accumulation of POC and MAOC.

Synergetic Effects of Soil Organic Matter Components During Interactions with Minerals

Mineral-associated soil organic matter (SOM) is critical for stabilizing organic carbon and mitigating climate change. However, mineral-SOM interactions at the molecular scale, particularly synergetic adsorption through organic-organic interaction on the mineral surface known as organic multilayering, remain poorly understood. This study investigates the impact of organic multilayering on mineral-SOM interactions, by integrating macroscale experiments and molecular-scale simulations that assess the individual and sequential adsorption of major SOM compounds-lauric acid (lipid), pentaglycine (amino acid), trehalose (carbohydrate), and lignin onto soil minerals. Ferrihydrite, Al-hydroxide, and calcite are exposed to SOM compounds to determine adsorption affinities and binding energies. Results show that lauric acid has 20-40 times higher Kd than pentaglycine, following the order Kd(ferrihydrite) > Kd(Al-hydroxide) ≫ Kd(calcite). Molecular-scale simulations confirm that lauric acid has a higher binding energy (30.8 kcal/mol) on ferrihydrite than pentaglycine (6.0 kcal/mol), attributed to lipid hydrophobicity. The lower binding energy of pentaglycine results from its hydrophilic amide groups, facilitating partitioning into water. Sequential experiments examine how the first layer of lipid or amino acid affects the adsorption of carbohydrate/lignin, which show little or no individual adsorption affinities. Macroscale results reveal that lipid and amino acid adsorption induce ferrihydrite particle repulsion increasing reactive surface area and enhancing carbohydrate/lignin adsorption independently and synergistically through organic multilayering. Molecular-scale results reveal that amino acid adsorbed on ferrihydrite interacts more readily with lignin macroaggregates (preformed in solution) than with individual lignin units, indicating organic multilayering via H-bonding. These findings reveal the molecular mechanisms of SOM-mineral interactions, crucial for enhancing soil carbon stabilization.

Recovery in soil carbon stocks but reduced carbon stabilization after near-natural restoration in degraded alpine meadows

Near-natural restoration is acknowledged as an effective strategy for enhancing soil organic carbon (SOC) sequestration in degraded grasslands. However, the alterations in SOC fractions, stability, and relative sequestration capacity after restoration of degraded alpine meadows remain uncertain. In this study, we utilized the degraded alpine meadows on the northeastern edge of the Tibetan Plateau as a research area, with grazing as the control (CK) and restoration of 20 years of banned grazing (BG) and growing season resting grazing (RG). We analyzed the characteristics of SOC, SOC fractions, recalcitrant index (RI), and relative capacity of soil C sequestration (SCScapacity) under near-natural restoration measures. The objective of this study was to assess the recovery of SOC following near-natural restoration. The results showed that soil water content (SWC), SOC, soil total nitrogen (TN), and soil total phosphorus (TP) increased, while bulk density (BD) decreased in the degraded alpine meadow after near-natural restoration. In addition, near-natural restoration led to significant increases in particulate organic carbon (POC), readily oxidizable carbon (ROC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) content (P < 0.05). The SOC stock significantly increased, while the RI decreased. Compared to RG, BG had a greater increase in SOC stock. The study showed that 20 years of near-natural restoration in degraded alpine meadows mainly enhanced soil active carbon pools, while short-term restoration did not increase soil carbon stability. Therefore, avoiding re-exposure to overgrazing is essential to maintaining the restoration effect.

Improvement of soil nutrient cycling by dominant plants in natural restoration of heavy metal polluted areas

Referring to the natural succession to restore polluted land is one of the most vital assignments to solving the environmental problems. However, there is little understanding of the natural restoration of nutrient biogeochemical cycles in abandoned land with severe metal pollution. To clarify the nutrient cycling process and the influence of organisms on it, we investigated the magnitude of rhizosphere effects on soil nitrogen (N), phosphorus (P) and sulphur (S) cycles in natural restoration of an abandoned metal mine, as well as the roles of plants and microorganisms in the nutrient cycles. Our data revealed that the rhizosphere had higher levels of ammoniation than non-rhizosphere soil at both stages of restoration. In the early stage, the rhizosphere had greater levels of inorganic phosphorus and organophosphorus solubilisation, as well as sulphite oxidation, compared to non-rhizosphere soil. The bacterial composition influenced the N and S cycles, while the fungal composition had the greatest effect on the P cycles. Furthermore, rhizosphere nutrition cycles and microbial communities altered according plant strategy. Overall, the plants that colonize the early stages of natural recovery demonstrate enhanced restoration of nutrient efficiency. These results contribute to further knowledge of nutrient recovery in mining areas, as well as suggestions for selecting remedial microorganisms and plants in metal-polluted environments.

Microbial necromass and glycoproteins for determining soil carbon formation under arbuscular mycorrhiza symbiosis

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil organic carbon (C) dynamics. Whether AMF promote soil C storage and stability is, however, largely unknown. Since microbial necromass C (MNC) and glomalin-related soil protein (GRSP) are stable microbial-derived C in soils, we therefore evaluated how AMF symbiosis alters both soil C pools and their contributions to soil organic C (SOC) under nitrogen fertilization, based on a 16-weeks mesocosm experiment using a mutant tomato with highly reduced AMF symbiosis. Results showed that SOC content is 4.5 % higher following AMF symbiosis. Additionally, the content of MNC and total GRSP were 47.5 % and 22.3 % higher under AMF symbiosis than at AMF absence, respectively. The accumulations of GRSP and microbial necromass in soil were closely associated with mineral-associated organic C and the abundance of AMF. The increased soil living microbial biomass under AMF symbiosis was mainly derived from AMF biomass, and fungal necromass C significantly contributed to SOC accumulation, as evidenced by the higher fungal:bacterial necromass C ratio under AMF symbiosis. On the contrary, bacterial necromass was degraded to compensate for the increased microbial nutrient demand because of the aggravated nutrient limitation under AMF symbiosis, leading to a decrease in bacterial necromass. Redundancy analysis showing that bacterial necromass was negatively correlated with soil C:N ratio supported this argument. Moreover, the relative change rate of total GRSP was consistently greater in nitrogen-limited soil than that of microbial necromass. Our findings suggested GRSP accumulates faster and contributes more to SOC pools under AMF symbiosis than microbial necromass. The positive correlation between the contributions of GRSP and MNC to SOC further provided valuable information in terms of enhancing our understanding of mechanisms underlying the maintenance of SOC stocks through microbial-derived C.

Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils

Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by 13C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg-1 d-1 to 0.092 mg kg-1 d-1, and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.

Gene Expression by a Model Fungus in the Ascomycota Provides Insight Into the Decay of Fungal Necromass

Dead fungal cells, known as necromass, are increasingly recognised as significant contributors to long-term soil carbon pools, yet the genes involved in necromass decomposition are poorly understood. In particular, how microorganisms degrade necromass with differing initial cell wall chemical compositions using carbohydrate-active enzymes (CAZymes) has not been well studied. Based on the frequent occurrence and high abundance of the fungal genus Trichoderma on decaying fungal necromass in situ, we grew Trichoderma reesei RUT-C30 on low and high melanin necromass of Hyaloscypha bicolor (Ascomycota) in liquid cultures and assessed T. reesei gene expression relative to each other and relative to glucose. Transcriptome data revealed that T. reesei up-regulated many genes (over 100; necromass versus glucose substrate) coding for CAZymes, including enzymes that would target individual layers of an Ascomycota fungal cell wall. We also observed differential expression of protease- and laccase-encoding genes on high versus low melanin necromass, highlighting a subset of genes (fewer than 15) possibly linked to the deconstruction of melanin, a cell wall constituent that limits necromass decay rates in nature. Collectively, these results advance our understanding of the genomic traits underpinning the rates and fates of carbon turnover in an understudied pool of Earth's belowground carbon, fungal necromass.

Mineral and Microbial Properties Drive the Formation of Mineral-Associated Organic Matter and Its Response to Increased Temperature

A comprehensive understanding of the formation of mineral-associated organic matter (MAOM) is a prerequisite for the sustainable management of soil carbon (C) and the development of effective long-term strategies for C sequestration in soils. Nevertheless, the precise manner by which microbial and mineral properties drive MAOM formation efficiency and its subsequent response to elevated temperature at the regional scale remains unclear. Here, we employed isotopically labelled laboratory incubations (at 15°C and 25°C) with soil samples from a ~3000 km transect across the Tibetan Plateau to elucidate the mechanisms underlying MAOM formation and its temperature response. The results indicated that both mineral protection and microbial properties were critical predictors of MAOM formation across the geographic gradient. The efficiency of MAOM formation was found to increase with the content of iron (Fe) oxides and their reactivity [i.e., the ratio of poorly crystalline Fe oxides to total Fe oxides (Feo:Fed)] but to decrease with the relative abundance of Gammaproteobacteria and Actinobacteria across the plateau. Moreover, a notable decline in MAOM formation efficiency was observed under elevated temperatures, which was concomitant with a reduction in the content and reactivity of Fe oxides, as well as the microbial assimilation of the labelled substrate. The attenuation of mineral-organic associations was identified as the primary factor contributing to the warming-induced reduction in MAOM formation. These findings highlight the necessity of incorporating organo-mineral associations and microbial properties into Earth System Models to accurately project soil C dynamics under changing climate.

Effect of 9-year water and nitrogen additions on microbial necromass carbon content at different soil depths and its main influencing factors

Microbial necromass carbon (MNC) is a major source of soil organic carbon (SOC) pool, significantly influencing soil carbon sequestration. The effects of long-term water and nitrogen addition on MNC in soils at different depths, as well as their interactions, remain poorly understood. In this study, we examined the influence of water addition (+51.67 mm), nitrogen addition (25, 50, 100 kg N ha-1 yr-1), and their interactions on MNC accumulation at different soil depths in temperate grasslands. The addition of water and nitrogen over nine years has been observed to exhibit a decreasing trend in the MNC at different soil depths. Notably, MNC in the topsoil layer (0-10 cm) decreased significantly by 18.56 % under low nitrogen addition treatment, while MNC in the subsoil layer (40-60 cm) declined significantly by 27.19 % under high nitrogen addition treatment. Fungal microbial necromass carbon (FNC) contributed 3.25 times more to SOC than bacterial microbial necromass carbon (BNC). In the 0-10 cm soil layer, MNC is primarily governed by both microbial attributes and the physicochemical properties of the soil, in the 20-40 cm soil layer, the physicochemical properties of the soil predominantly control MNC, in the 40-60 cm layer, microbial characteristics exert a more significant influence on MNC. Collectively, our observations suggest that soil MNC decreased with the addition of water and nitrogen in the 0-60 cm soil slope, which could enable the accurate prediction of global change impacts on the accumulation of soil carbon, thus facilitating the implementation of strategies to augment soil carbon sequestration.

Necromass responses to warming: A faster microbial turnover in favor of soil carbon stabilisation

Microbial byproducts and residues (hereafter 'necromass') potentially play the most critical role in soil organic carbon (SOC) sequestration. However, little is known about the influence of climate warming on necromass accumulation in the agroecosystem and the underlying mechanisms associated with microbial life strategies. In order to address these knowledge gaps, we used amino sugars as biomarkers of microbial necromass, and investigated their variation through an 8-year trial in an agroecosystem with two warming levels (+1.6 and + 3.2 °C) compared to ambient temperature. The results showed that the lower warming level had no impact on total microbial necromass carbon. Conversely, warming the soil 3.2 °C above ambient increased total microbial necromass by 17 % and its contribution to SOC by 21.3 %, mainly by increasing fungal necromass (+19.8 %), whereas +3.2 °C warming had no impact on bacterial necromass. At the phylum level, compared with the ambient control, +3.2 °C warming induced an increase in the abundance of Proteobacteria and a decrease in both Acidobacteria and Actinobacteria, whereas in the fungal community, Ascomycota increased and Mortierellomycota decreased. This indicates that r-strategists outcompete K-strategists in warmer climates, which led to increased microbial necromass production and accumulation, as supported by the positive correlation between r-strategists and microbial necromass. Stronger microbial competition for resources also resulted in a higher biomass turnover rate, greater cell death, and greater production of microbial necromass. This was supported by the lower bacterial and fungal network complexity and trophic links under warming conditions. In addition, the necromass generated from accelerated microbial turnover further offsets warming-induced deceases in microbial biomass. Consequently, bulk SOC did not change, despite microbial necromass having a much greater response to warming than the soil C pool. Therefore, future climate warming may influence the composition and persistence of SOC during microbial degradation.

Bacterial necromass as the main source of organic matter in saline soils

Soil salinity poses a major threat to crop growth, microbial activity, and organic matter accumulation in agroecosystems in arid and semiarid regions. The limitations of carbon (C) accrual due to salinity can be partly mitigated by the application of organic fertilizers. Although microorganisms are crucial for soil organic carbon (SOC) stabilization, the relationships between living and dead microbial C pools and the community features of SOC accrual in saline soils are not known. A two-year field experiment was conducted to examine the effects of organic fertilizers on the microbial regulatory mechanisms of C sequestration in saline soil (chloride-sulfate salinity). Compared to manure addition alone, manure plus commercial humic acid increased SOC stock by 11% and decreased CO2 emissions by 10%, consequently facilitated soil C sequestration. We explain these results by greater bacterial necromass formation due to the dominance of r-strategists with faster turnover rate (growth and death), as well as larger necromass stability as supported by the increased aggregate stability under the addition of humic acids with manure. Humic acids increased the abundance of bacterial phylum Proteobacteria (copiotrophs) and decreased Acidobacteria (oligotrophs) compared with straw, indicating that r-strategists outcompeted K-strategists, leading to bacterial necromass accumulation. With larger C/N ratio (88), straw increased leucine aminopeptidase to mine N-rich substrates (i.e., from necromass and soil organic matter) and consequently reduced SOC stock by 8%. The decreased salinity and increased organic C availability under straw with manure addition also led to a 13% higher CO2 flux compared with manure application alone. Thus, humic acids added with manure benefited to SOC accumulation by raising bacterial necromass C and reducing CO2 emissions.

Microbial trait multifunctionality drives soil organic matter formation potential

Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.

Microbial and mineral interactions decouple litter quality from soil organic matter formation

Current understanding of soil carbon dynamics suggests that plant litter quality and soil mineralogy control the formation of mineral-associated soil organic carbon (SOC). Due to more efficient microbial anabolism, high-quality litter may produce more microbial residues for stabilisation on mineral surfaces. To test these fundamental concepts, we manipulate soil mineralogy using pristine minerals, characterise microbial communities and use stable isotopes to measure decomposition of low- and high-quality litter and mineral stabilisation of litter-C. We find that high-quality litter leads to less (not more) efficient formation of mineral-associated SOC due to soil microbial community shifts which lower carbon use efficiency. Low-quality litter enhances loss of pre-existing SOC resulting in no effect of litter quality on total mineral-associated SOC. However, mineral-associated SOC formation is primarily controlled by soil mineralogy. These findings refute the hypothesis that high-quality plant litters form mineral-associated SOC most efficiently and advance our understanding of how mineralogy and litter-microbial interactions regulate SOC formation.

Maize and soybean rotation benefits soil quality and organic carbon stock

Soybean and maize rotation has been recommended as a promising strategy to maximize crop yield. However, the impacts of soybean-maize rotation, and particularly the frequency of soybean inclusion, on soil quality and carbon (C) stock need to explored. We conducted an 8-year field experiment of randomized design in Northeast China with four cropping systems as continuous soybean (S), continuous maize (M), soybean-maize rotation (SM), and soybean-maize-maize rotation (SMM). The results showed that the soil quality index, soil ecosystem multifunctionality (EMF), and C stock under crop rotation (SM and SMM) were 5.4-23.5%, 13.1-22.6%, and 9.3-29.4% higher than those under continuous cropping (M and S), respectively. Additionally, the increased frequency of soybean in the rotation increased soil EMF by 14.8% due to higher soil enzyme activities and available N. Notably, the soybean-maize rotation alleviated microbial nitrogen (N) limitation compared to continuous cropping, due to stimulated C, N, and P acquisition by enzyme activities. Furthermore, the soil quality index correlated positively with C stock in the topsoil. The accumulation rates of soil organic C and total N were higher by 0.39 and 0.14 g kg-1 year-1 in SMM than in SM, respectively. Therefore, scientifically based soybean frequency is an effective approach to enhance soil organic C in soybean and maize rotation. In conclusion, soybean-maize rotation improves soil quality compared to monoculture, and a reduced frequency of soybean within the rotation (SMM) is beneficial for C and N storage.

Microbial necromass contribution to soil carbon storage via community assembly processes

Soil organic matter has been well acknowledged as a natural solution to mitigate climate change and to maintain agricultural productivity. Microbial necromass is an important contributor to soil organic carbon (SOC) storage, and serves as a resource pool for microbial utilization. The trade-off between microbial births/deaths and resource acquisition might influence the fate of microbial necromass in the SOC pool, which remains poorly understood. We coupled soil microbial assembly with microbial necromass contribution to SOC on a long-term, no-till (NT) farm that received maize (Zea mays L.) stover mulching in amounts of 0 %, 33 %, 67 %, and 100 % for 8 y. We characterized soil microbial assembly using the Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP), and microbial necromass using its biomarker amino sugars. We found that 100 % maize stover mulching (NT100) was associated with significantly lower amino sugars (66.4 mg g-1 SOC) than the other treatments (>70 mg g-1 SOC). Bacterial and fungal communities responded divergently to maize stover mulching: bacterial communities were positive for phylogenetic diversity, while fungal communities were positive for taxonomic richness. Soil bacterial communities influenced microbial necromass contribution to SOC through determinism on certain phylogenetic groups and bacterial bin composition, while fungal communities impacted SOC accumulation through taxonomic richness, which is enhanced by the positive contribution of dispersal limitation-dominated saprotrophic guilds. The prevalence of homogeneous selection and dispersal limitation on microbial cell wall-degrading bacteria, specifically Chitinophagaceae, along with increased soil fungal richness and interactions, might induce the decreased microbial necromass contribution to SOC under NT100. Our findings shed new light on the role of microbial assembly in shaping the dynamics of microbial necromass and SOC storage. This advances our understanding of the biological mechanisms that underpin microbial necromass associated with SOC storage, with implications for sustainable agriculture and mitigation of climate change.

Grassland degraded patchiness reduces microbial necromass content but increases contribution to soil organic carbon accumulation

Plant and microbially derived carbon (C) are the two major sources of soil organic carbon (SOC), and their ratio impacts SOC composition, accumulation, stability, and turnover. The contributions of and the key factors defining the plant and microbial C in SOC with grassland patches are not well known. Here, we aim to address this issue by analyzing lignin phenols, amino sugars, glomalin-related soil proteins (GRSP), enzyme activities, particulate organic carbon (POC), and mineral-associated organic carbon (MAOC). Shrubby patches showed increased SOC and POC due to higher plant inputs, thereby stimulating plant-derived C (e.g., lignin phenol) accumulation. While degraded and exposed patches exhibited higher microbially derived C due to reduced plant input. After grassland degradation, POC content decreased faster than MAOC, and plant biomarkers (lignin phenols) declined faster than microbial biomarkers (amino sugars). As grassland degradation intensified, microbial necromass C and GRSP (gelling agents) increased their contribution to SOC formation. Grassland degradation stimulated the stabilization of microbially derived C in the form of MAOC. Further analyses revealed that microorganisms have a C and P co-limitation, stimulating the recycling of necromass, resulting in the proportion of microbial necromass C in the SOC remaining essentially stable with grassland degradation. Overall, with the grassland degradation, the relative proportion of the plant component decreases while than of the microbial component increases and existed in the form of MAOC. This is attributed to the physical protection of SOC by GRSP cementation. Therefore, different sources of SOC should be considered in evaluating SOC responses to grassland degradation, which has important implications for predicting dynamics in SOC under climate change and anthropogenic factors.