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.

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.

Soil organic carbon stabilization is influenced by microbial diversity and temperature

The stabilization of soil organic carbon (SOC) is influenced by soil microbes and environmental factors, particularly temperature, which significantly affects SOC decomposition. This study investigates the effects of temperature (ambient: 25 °C; elevated: 27.5 °C) and soil microbial diversity (low, medium, and high) on the formation of stabilized SOC, focusing on mineral-associated organic carbon (MAOC) and water-stable aggregates, through a 75-day model soil incubation experiment. We measured water-stable aggregates, microbial respiration, and SOC in different fractions. Our results demonstrate that microbial diversity is crucial for SOC mineralization; low diversity resulted in 3.93-6.26% lower total carbon and 8.05-17.32% lower particulate organic carbon (POC) compared to medium and high diversity under the same temperature. While total MAOC was unaffected by temperature and microbial diversity, macroaggregate-occluded MAOC decreased by 8.78%, 38.36% and 9.40% under elevated temperature for low, medium and high diversity, respectively, likely driven by decreased macroaggregate formation. A negative correlation between macroaggregate-occluded POC and microbial respiration (r= -0.37, p < 0.05) suggested microbial decomposition of POC within macroaggregates contributed to respiration, with a portion of the decomposed POC potentially stabilized as microbial-derived MAOC. Notably, soils with medium microbial diversity exhibited the highest levels of both macroaggregate-occluded POC and MAOC at ambient temperature; however, elevated temperature disrupted this stabilization, reducing both POC retention and MAOC accumulation within macroaggregates. These findings underscore the temperature-sensitive interplay between microbial diversity and SOC stabilization, highlighting the need to disentangle microbial pathways governing C dynamics under climate change.

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.

Long-term free-air-CO2-enrichment increases carbon distribution in the stable fraction in the deep layer of non-clay soils

Elevated CO2 (eCO2) in the atmosphere can increase plant C input into soils. However, in dryland cropping systems, it remains unclear how eCO2 may alter soil organic C content and stability in relation to potential changes in microbial community composition and whether these changes may depend on soil type and depth. Using an eight-year free-air-CO2-enrichment (SoilFACE) system, this study addressed these questions in three farming soils including a sandy Calcarosol, a clay Vertosol and a silt loam Chromosol at depths of 0-40 cm. Long-term eCO2 did not change soil C content or its distribution in different C fractions in the top 30-cm soil. The majority of the relatively abundant bacterial taxa significantly affected by eCO2 in the 0-10 cm layer were copiotrophic; this also occurred to fungal community, except for the Calcarosol where some saprotrophs showed a decreasing trend. These changes in microbial taxa indicate that eCO2 accelerated the decomposition of both new and pre-existing C pools in the topsoil. Although eCO2 did not change soil C content in the 30-40 cm layer, it increased soil C content in the stable C fraction associated with particles < 50 μm in the Calcarosol (by 39%) and particles < 2 μm in the Chromosol (by 29%). In the 30-40 cm layer of the Calcarosol, many fungal saprotrophs were enriched, and the abundance of fungal community increased under eCO2. Further investigation is warranted on whether the enhanced stability subsoil C under eCO2 results from the leaching of stable organic molecules from the topsoil to the subsoil for buildup in the non-clay Calcarosol and Chromosol. Overall, these findings suggest that eCO2 is likely to enhance soil C stability in the deeper parts of the profile of non-clay soils.

From carrion to soil: microbial recycling of animal carcasses

Decomposer microbial communities are gatekeepers in the redistribution of carbon and nutrients from dead animals (carrion) to terrestrial ecosystems. The flush of decomposition products from a carcass creates a hot spot of microbial activity in the soil below, and the animal's microbiome is released into the environment, mixing with soil communities. Changes in soil physicochemistry, especially reduced oxygen, temporarily constrain microbial nutrient cycling, and influence the timing of these processes and the fate of carrion resources. Carcass-related factors, such as mass, tissue composition, or even microbiome composition may also influence the functional assembly and succession of decomposer communities. Understanding these local scale microbially mediated processes is important for predicting consequences of carrion decomposition beyond the hot spot and hot moment.

Old but not ancient: Rock-leached organic carbon drives groundwater microbiomes

More than 90% of earth's microbial biomass resides in the continental subsurface, where sedimentary rocks provide the largest source of organic carbon (C). While many studies indicate microbial utilization of fossil C sources, the extent to which rock-organic C is driving microbial activities in aquifers remains largely unknown. Here we incubated oxic and anoxic groundwater with crushed carbonate rocks from the host aquifer and an outcrop rock of the unsaturated zone characterized by higher organic C content, and compared the natural abundance of radiocarbon (14C) of available C pools and microbial biomarkers. The ancient rocks surprisingly released organic substances with up to 72.6 ± 0.3% modern C into the groundwater, suggesting leachable fresh organic material from surface transport was preserved within rock fractures. Over half of the rock-leached compounds were also found in the original groundwater dissolved organic carbon (DOC), indicating in situ release of material stored in rock fractures through weathering processes. In addition to aliphatic and aromatic hydrocarbons, rock-leachates were rich in lipids, peptides, and carbohydrates. Radiocarbon analysis of phospholipid-derived fatty acids showed a rapid microbial response to this 'younger' organic material, comprising up to 31% (anoxic) and 51% (oxic) of their biomass C from the rock-leachate after 18 days of incubation. Predictive functional profiling of rock-enriched taxa, including species of Desulfosporosinus, Ferribacterium and Rhodoferax, also suggested metabolic potential for aliphatic and aromatic hydrocarbon degradation. PLFAs of the original groundwater were highly 14C-depleted, indicating utilization of a mixture of fossil and 'younger' C sources. Our findings suggest that carbonate rocks act as temporal sink for 'younger' organic matter, that leaches with fossil hydrocarbons from sedimentary rocks, driving microbial metabolism in subsurface ecosystems.

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.

Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.

Dynamics of bacterial growth, and life-history tradeoffs, explain differences in soil carbon cycling due to land-use

Soil contains a considerable fraction of Earth's organic carbon. Bacterial growth and mortality drive the microbial carbon pump, influencing carbon use efficiency and necromass production, key determinants for organic carbon persistence in soils. However, bacterial growth dynamics in soil are poorly characterized. We used an internal standard approach to normalize 16S ribosomal RNA gene sequencing data allowing us to quantify growth dynamics for 30 days following plant litter input to soil. We show that clustering taxa into three groups optimized variation of bacterial growth parameters in situ. These three clusters differed significantly with respect to their lag time, growth rate, growth duration, and change in abundance due to growth (ΔNg) and mortality (ΔNd), matching predictions of Grime's CSR life-history framework. In addition, we show a striking relationship between ΔNg and ΔNd, which reveals that growth in soil is tightly coupled to death. This result suggests a fitness paradox whereby some bacteria can optimize fitness in soil by minimizing mortality rather than maximizing growth. We hypothesized that land-use constrains microbial growth dynamics by favoring different life-history strategies and that these constraints control carbon mineralization. We show that life-history groups vary in prevalence with respect to land-use, and that bacterial growth dynamics correlated with carbon mineralization rate and net growth efficiency. Meadow soil supported more bacterial growth, greater mortality, and higher growth efficiency than agricultural soils, pointing toward more efficient conversion of plant litter into microbial necromass, which should promote long-term C stabilization.

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.

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.

The Fungal Community Structure Regulates Elevational Variations in Soil Organic Carbon Fractions in a Wugong Mountain Meadow

Soil organic carbon (SOC) fractions are vital intrinsic indicators of SOC stability, and soil fungi are the key drivers of soil carbon cycling. However, variations in SOC fractions along an elevational gradient in mountain meadows and the role of the fungal community in regulating these variations are largely unknown, especially in subtropical areas. In this study, an elevation gradient experiment (with experimental sites at 1500, 1700, and 1900 m) was set up in a Miscanthus sinensis community in a meadow on Wugong Mountain, Southeast China, to clarify the effects of elevation on soil fungal community composition, microbial residue carbon, and SOC fractions. The results showed that the contribution of soil microbial residue carbon to SOC was only 16.1%, and the contribution of soil fungal residue carbon to SOC (15.3%) was far greater than that of bacterial residue carbon (0.3%). An increase in elevation changed the fungal community structure and diversity, especially in the topsoil (0-20 cm depth) compared with that in the subsoil (20-40 cm depth), but did not affect fungal residue carbon in the two soil layers. When separating SOC into the fractions mineral-associated organic carbon (MAOC) and particulate organic carbon (POC), we found that the contribution of MAOC (66.6%) to SOC was significantly higher than that of POC (20.6%). Although an increased elevation did not affect the SOC concentration, it significantly changed the SOC fractions in the topsoil and subsoil. The soil POC concentration and its contribution to SOC increased with an increasing elevation, whereas soil MAOC showed the opposite response. The elevational variations in SOC fractions and the POC/MAOC ratio were co-regulated by the fungal community structure and total nitrogen. Our results suggested that SOC stabilization in mountain meadows decreases with an increasing elevation and is driven by the fungal community structure, providing scientific guidance for SOC sequestration and stability in mountain meadows in subtropical areas.

Rice-crayfish farming system promote subsoil microbial residual carbon accumulation and stabilization by mediating microbial metabolism process

Rice-crayfish farming systems (RCs) can help mitigate climate change by enhancing soil organic carbon (SOC) sequestration. However, the mechanisms that govern the responses of microbial residues carbon (MRC), a key component of SOC, in RCs are not fully understood. We conducted a 6-year field experiment comparing RCs and rice monoculture systems (RMs). Specifically, we explored how MRC formation and stabilization differ between the two systems and how those differences are linked to changes in the metabolic processes of microbes. Results showed that MRC levels in RCs were 5.2 % and 40.0 % higher in the topsoil and subsoil, respectively, compared to RMs, indicating depth-dependent effects. Notably, MRC accumulation and stabilization in RCs were promoted through a cascade of processes of dissolved organic carbon (DOC) accessibility-microbial metabolism-mineral protection. In addition, the mechanism of MRC accumulation in subsoil differed between the two systems. Specifically, RMs improved accessibility of DOC by reducing humification and aromaticity of subsoil DOC, which helped microbes access to resources at lower cost. This decreased the respiration rate of microbes, thereby increasing microbial carbon pump (MCP) efficiency and thus promoting MRC accumulation. By contrast, the crayfish in RCs facilitated carbon exchange between topsoil and subsoil through their burrowing behaviors. This increased carbon allocation for microbial metabolism in the subsoil, supporting a larger microbial population and thus enhancing the MCP capacity, while reducing MRC re-decomposition via enhanced mineral protection, further increasing subsoil MRC accumulation. That is, MRC accumulation in the subsoil of RCs was predominantly driven by microbial population numbers (MCP capacity) whereas that of RMs was mostly driven by microbial anabolic efficacy (MCP efficiency). Our findings reveal a key mechanism by which RCs promoted soil MRC accumulation and stabilization, highlighting the potential role of DOC accessibility-microbial metabolism-mineral protection pathway in regulating MRC accumulation and stabilization.

Long-term sheep grazing reduces fungal necromass carbon contribution to soil organic carbon in the desert steppe

Grazing has been shown to impact the soil environment and microbial necromass carbon (MNC), which in turn regulates soil organic carbon (SOC). However, the carbon sequestration potential of fungi and bacteria under different stocking rates remains unclear, limiting our understanding of soil carbon sequestration in grazing management. In 2004, we established grazing experiments in the desert steppe of northern China with four stocking rates. Our findings indicate that MNC decreased under moderate and heavy grazing, while light grazing did not significantly differ from no grazing. Notably, the reduction in fungal necromass carbon, rather than bacterial necromass carbon, was primarily responsible for the decreased contribution of MNC to SOC. This difference is attributed to the varying effects of sheep grazing on fungal and bacterial community characteristics, including richness, diversity, and composition. Thus, to accurately predict carbon dynamics in grassland ecosystems, it is essential to consider that the ecological impacts and carbon sequestration potential of microbial communities may vary with different grazing management practices.

Effect of mineral and organic fertilizer on N dynamics upon erosion-induced topsoil dilution

Erosion-induced topsoil dilution strongly affects cropland biogeochemistry and is associated with a negative effect on soil health and crop productivity. While its impact on soil C cycling has been widely recognized, there is little information about its impact on soil N cycling and N fertilizer dynamics. Here, we studied three factors potentially influencing N cycling and N fertilizer dynamics in cropping systems, namely: 1.) soil type, 2.) erosion-induced topsoil dilution and 3.) N fertilizer form, in a full-factorial pot experiment using canola plants. We studied three erosion affected soil types (Luvisol, eroded Luvisol, calcaric Regosol) and performed topsoil dilution in all three soils by admixing 20 % of the respective subsoil into its topsoil. N fertilizer dynamics were investigated using either mineral (calcium ammonium nitrate) or organic (biogas digestate) fertilizer, labeled with 15N. The fertilizer 15N recovery and the distribution of the fertilizer N in different soil fractions was quantified after plant maturity. Fertilizer N dynamics and utilization were influenced by all three factors investigated. 15N recovery in the plant-soil system was higher and fertilizer N utilization was lower in the treatments with diluted topsoil than in the non-diluted controls. Similarly, plants of the organic fertilizer N treatments took up significantly less fertilizer N in comparison to mineral fertilizer treatments. Both topsoil dilution and organic fertilizer application promoted 15N recovery and N accumulation in the soil fractions, with strong differences between soil types. Our study reveals an innovative insight: topsoil dilution due to soil erosion has a negligible impact on N cycling and dynamics in the plant-soil system. The crucial factors influencing these processes are found to be the choice of fertilizer form and the specific soil type. Recognizing these aspects is essential for a precise and comprehensive assessment of the environmental continuum, emphasizing the novelty of our findings.

Microbial necromass facilitated the humification process through amino sugar reactions during the co-composting of cow manure plus sawdust

Humus (HS) reservoirs can embed microbial necromass (including cell wall components that are intact or with varying degrees of fragmentation) in small pores, raising widespread concerns about the potential for C/N interception and stability in composting systems. In this study, fresh cow manure and sawdust were used for microbial solid fermentation, and the significance of microbial residues in promoting humification was elucidated by measuring their physicochemical properties and analyzing their microbial informatics. These results showed that the stimulation of external carbon sources (NaHCO3) led to an increase in the accumulation of bacterial necromass C/N from 6.19 and 0.91 µg/mg to 21.57 and 3.20 µg/mg, respectively. Additionally, fungal necromass C/N values were about 3 times higher than the initial values. This contributed to the increase in HS content and the increased condensation of polysaccharides and nitrogen-containing compounds during maturation. The formation of cellular debris mainly depends on the enrichment of Actinobacteria, Proteobacteria, Ascomycota, and Chytridiomycota. Furthermore, Euryarchaeota was the core functional microorganism secreting cell wall lytic enzymes (including AA3, AA7, GH23, and GH15). In conclusion, this study comprehensively analyzed the transformation mechanisms of cellular residuals at different profile scales, providing new insights into C/N cycles and sequestration.

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

Long-term vegetation restoration promotes lignin phenol preservation and microbial anabolism in forest plantations: Implications for soil organic carbon dynamics

Vegetation restoration contributes to soil organic carbon (C; SOC) sequestration through the accumulation of plant and microbial residues, but the mechanisms underlying this microbially mediated process are not well resolved. To depict the dynamics of plant- and microbial-derived C in restored forest ecosystems, soil samples were collected from Robinia pseudoacacia plantations of different stand ages (15, 25, 35, 45 years old) established on degraded wheat fields. The results showed that the degree of lignin phenol oxidation decreased with increasing stand age (P < 0.05), and hemicellulose-degrading genes were detected at higher relative abundances than other functional gene categories, indicating selective preservation of recalcitrant lignin phenols. Despite both glucosamine (R2 = 0.61, P < 0.001) and muramic acid (R2 = 0.37, P < 0.001) contents trending upward over time, fungal residual C accounted for a greater proportion of SOC compared with bacterial residual C. Accordingly, fungal residual C, which exhibited a similar response pattern as total microbial residual C to vegetation restoration, was considered a major contributor to the SOC pool. These results provided evidence that long-term vegetation restoration enhanced SOC sequestration in R. pseudoacacia forest by promoting the preservation of plant-derived lignin phenols and concomitant microbial anabolism. Partial least squares-discriminant analysis identified two important ecological clusters (i.e., modules) in the fungal network that profoundly influenced lignin phenol oxidation (P < 0.05) and microbial residual C accumulation (P < 0.01). Among the dominant taxa in microbial networks, the bacterial phyla Proteobacteria and Acidobacteriota had potential to degrade recalcitrant C compounds (e.g., cellulose, lignin), whereas the fungal phylum Ascomycota could outcompete for labile C fractions (e.g., dissolved organic C). Findings of this study can enable a mechanistic understanding of SOC stability driven by microbial turnover in restored forest ecosystems.

Global synthesis on the response of soil microbial necromass carbon to climate-smart agriculture

Climate-smart agriculture (CSA) supports the sustainability of crop production and food security, and benefiting soil carbon storage. Despite the critical importance of microorganisms in the carbon cycle, systematic investigations on the influence of CSA on soil microbial necromass carbon and its driving factors are still limited. We evaluated 472 observations from 73 peer-reviewed articles to show that, compared to conventional practice, CSA generally increased soil microbial necromass carbon concentrations by 18.24%. These benefits to soil microbial necromass carbon, as assessed by amino sugar biomarkers, are complex and influenced by a variety of soil, climatic, spatial, and biological factors. Changes in living microbial biomass are the most significant predictor of total, fungal, and bacterial necromass carbon affected by CSA; in 61.9%-67.3% of paired observations, the CSA measures simultaneously increased living microbial biomass and microbial necromass carbon. Land restoration and nutrient management therein largely promoted microbial necromass carbon storage, while cover crop has a minor effect. Additionally, the effects were directly influenced by elevation and mean annual temperature, and indirectly by soil texture and initial organic carbon content. In the optimal scenario, the potential global carbon accrual rate of CSA through microbial necromass is approximately 980 Mt C year-1, assuming organic amendment is included following conservation tillage and appropriate land restoration. In conclusion, our study suggests that increasing soil microbial necromass carbon through CSA provides a vital way of mitigating carbon loss. This emphasizes the invisible yet significant influence of soil microbial anabolic activity on global carbon dynamics.

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Spatial variation and controls of soil microbial necromass carbon in a tropical montane rainforest

Soil microbial necromass carbon is an important component of the soil organic carbon (SOC) pool which helps to improve soil fertility and texture. However, the spatial pattern and variation mechanisms of fungal- and bacterial-derived necromass carbon at local scales in tropical rainforests are uncertain. This study showed that microbial necromass carbon and its proportion in SOC in tropical montane rainforest exhibited large spatial variation and significant autocorrelation, with significant high-high and low-low clustering patterns. Microbial necromass carbon accounted for approximately one-third of SOC, and the fungal-derived microbial necromass carbon and its proportion in SOC were, on average, approximately five times greater than those of bacterial-derived necromass. Structural equation models indicated that soil properties (SOC, total nitrogen, total phosphorus) and topographic features (elevation, convexity, and aspect) had significant positive effects on microbial necromass carbon concentrations, but negative effects on its proportions in SOC (especially the carbon:nitrogen ratio). Plant biomass also had significant negative effects on the proportion of microbial necromass carbon in SOC, but was not correlated with its concentration. The different spatial variation mechanisms of microbial necromass carbon and their proportions in SOC are possibly related to a slower accumulation rate of microbial necromass carbon than of plant-derived organic carbon. Geographic spatial correlations can significantly improve the microbial necromass carbon model fit, and low sampling resolution may lead to large uncertainties in estimating soil carbon dynamics at specific sites. Our work will be valuable for understanding microbial necromass carbon variation in tropical forests and soil carbon prediction model construction with microbial participation.

High stocking rates effects in continuous season long grazing reduces the contribution of microbial necromass to soil organic carbon in a semi-arid grassland in Inner Mongolia

Livestock grazing strongly influences the accumulation of soil organic carbon (SOC) in grasslands. However, whether the changes occurring in SOC content under different intensities of continuous summer long grazing are associated with the changes in microbially-derived necromass C remains unclear. Here, we established a sheep grazing experiment in northern China in 2004 with four different stocking rates. Soil samples were collected after 17 years of grazing and analyzed for physical, chemical, and microbial characteristics. Grazing decreased SOC and microbial necromass carbon (MNC). Notably, grazing also diminished contributions of MNC to SOC. MNC declined with decreasing plant carbon inputs with degradation of the soil environment. Direct reductions in microbial necromass C, which indirectly reduced SOC, resulted from reduced in plant C inputs and microbial abundance and diversity. Our study highlights the key role of stocking rate in governing microbial necromass C and SOC and the complex relationships these variables.

Long-term biogas slurry application increases microbial necromass but not plant lignin contribution to soil organic carbon in paddy soils as regulated by fungal community

Biogas slurry (BS) is widely considered as a source of organic matter and nutrients for improving soil organic carbon (SOC) sequestration and crop production in agroecosystems. Microbial necromass C (MNC) is considered one of the major precursors of SOC sequestration, which is regulated by soil microbial anabolism and catabolism. However, the microbial mechanisms through which BS application increases SOC accumulation in paddy soils have not yet been elucidated. A 12-year field experiment with four treatments (CK, no fertilizers; CF, chemical fertilizer application; BS1 and BS2, biogas slurry application at two nitrogen rates from BS) was conducted in rice paddy fields. The results showed that long-term BS application had no effect on lignin phenols proportion in SOC relative to CF. In contrast, BS application elevated the MNC contribution to SOC by 15.5-20.5 % compared with the CF treatment. The proportion of fungal necromass C (FNC) to SOC increased by 16.0 % under BS1 and by 25.8 % under BS2 compared with the CF treatment, while no significant difference in bacterial necromass C (BNC) contribution to SOC was observed between the BS and CF treatments. The MNC was more closely correlated with fungal community structures than with bacterial community structures. We further found that fungal genera, Mortierella and Ciliophora, mainly regulated the MNC, FNC and BNC accumulation. Collectively, our results highlighted that fungi play a vital role in SOC storage in paddy soils by regulating MNC formation and accumulation under long-term BS application.

Response of the C-fixing bacteria community to precipitation changes and its impact on bacterial necromass accumulation in semiarid grassland

Climate change-induced warming has the potential to intensify drought conditions in certain regions, resulting in uneven precipitation patterns. However, the impact of precipitation-induced changes on soil C-fixing bacterial community composition to changes and their subsequent effect on the accumulation of microbial necromass in the soil remains unclear. To address this knowledge gap, we conducted an in-situ simulated precipitation control experiment in semi-arid grasslands, encompassing five primary precipitation gradients: ambient precipitation as a control (contr), decreased precipitation by 80% and 40% (DP80, DP40), and increased precipitation by 40% and 80% (IP80, IP40). Our findings indicate that while an increase in precipitation promotes greater total bacterial diversity, it reduces the diversity of cbbM-harboring bacteria. The dominance of drought-tolerant Proteobacteria within the cbbM-harboring bacterial community was responsible for the observed increase in their relative abundance, ranging from 8.9% to 15.6%, under conditions of decreased precipitation. In arid environments characterized by limited soil moisture and nutrient availability, certain dominant genera such as Thiobacillus, Sulfuritalea, and Halothiobacillus, which possess cbbM genes, exhibit strong synergistic effects with other bacteria, thereby leading to a high nutrient use efficiency. Linear regression analysis shows that bacterial necromass C was significantly negatively correlated with cbbM-harboring bacterial diversity but positively correlated with cbbM-harboring bacterial community composition. Consequently, in the extreme drought environment of DP80, the contribution of bacterial necromass C to SOC was dramatically reduced by 75% relative to the control. Although bacterial necromass C was preferentially consumed as nutrients and energy for microorganisms, C-fixing microorganisms supplemented the soil C pool by assimilating atmospheric CO2. Bacterial necromass was primarily controlled by accessible C and N rather than by the total bacterial community composition and relative abundance. Our results provide compelling evidence for the critical role of the composition of the bacterial community and its necromass in the accumulation of SOC in semiarid grassland ecosystems.

Cross-scale spatial variability and associations of carbon pools provide insight into regulating carbon sequestration in tropical montane rainforests

The spatial distribution of plant, soil, and microbial carbon pools, along with their intricate interactions, presents a great challenge for the current carbon cycle research. However, it is not clear what are the characteristics of the spatial variability of these carbon pools, particularly their cross-scale relationships. We investigated the cross-scale spatial variability of microbial necromass carbon (MNC), soil organic carbon (SOC) and plant biomass (PB), as well as their correlation in a tropical montane rainforest using multifractal analysis. The results showed multifractal spatial variations of MNC, SOC, and PB, demonstrating their adherence to power-law scaling. MNC, especially low MNC, exhibited stronger spatial heterogeneity and weaker evenness compared with SOC and PB. The cross-scale correlation between MNC and SOC was stronger than their correlations at the measurement scale. Furthermore, the cross-scale spatial variability of MNC and SOC exhibited stronger and more stable correlations than those with PB. Additionally, this research suggests that when SOC and PB are both low, it is advisable for reforestations to potentiate MNC formation, whereas when both SOC and PB are high some thinning can be advisable to favour MNC formation. Thus, these results support the utilization of management measures such as reforestation or thinning as nature-based solutions to regulate carbon sequestration capacity of tropical forests by affecting the correlations among various carbon pools.

Microbial Necromass, Lignin, and Glycoproteins for Determining and Optimizing Blue Carbon Formation

Coastal wetlands contribute to the mitigation of climate change through the sequestration of "blue carbon". Microbial necromass, lignin, and glycoproteins (i.e., glomalin-related soil proteins (GRSP)), as important components of soil organic carbon (SOC), are sensitive to environmental change. However, their contributions to blue carbon formation and the underlying factors remain largely unresolved. To address this paucity of knowledge, we investigated their contributions to blue carbon formation along a salinity gradient in coastal marshes. Our results revealed decreasing contributions of microbial necromass and lignin to blue carbon as the salinity increased, while GRSP showed an opposite trend. Using random forest models, we showed that their contributions to SOC were dependent on microbial biomass and resource stoichiometry. In N-limited saline soils, contributions of microbial necromass to SOC decreased due to increased N-acquisition enzyme activity. Decreases in lignin contributions were linked to reduced mineral protection offered by short-range-ordered Fe (FeSRO). Partial least-squares path modeling (PLS-PM) further indicated that GRSP could increase microbial necromass and lignin formation by enhancing mineral protection. Our findings have implications for improving the accumulation of refractory and mineral-bound organic matter in coastal wetlands, considering the current scenario of heightened nutrient discharge and sea-level rise.

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances

Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.

Can we manage microbial systems to enhance carbon storage?

Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.

Contribution of microbial activity and vegetation cover to the spatial distribution of soil respiration in mountains

The patterns of change in bioclimatic conditions determine the vegetation cover and soil properties along the altitudinal gradient. Together, these factors control the spatial variability of soil respiration (R_S) in mountainous areas. The underlying mechanisms, which are poorly understood, shape the resulting surface CO₂ flux in these ecosystems. We aimed to investigate the spatial variability of R_S and its drivers on the northeastern slope of the Northwest Caucasus Mountains, Russia (1,260-2,480 m a.s.l.), in mixed, fir, and deciduous forests, as well as subalpine and alpine meadows. R_S was measured simultaneously in each ecosystem at 12 randomly distributed points using the closed static chamber technique. After the measurements, topsoil samples (0-10 cm) were collected under each chamber (n = 60). Several soil physicochemical, microbial, and vegetation indices were assessed as potential drivers of R_S. We tested two hypotheses: (i) the spatial variability of R_S is higher in forests than in grasslands; and (ii) the spatial variability of R_S in forests is mainly due to soil microbial activity, whereas in grasslands, it is mainly due to vegetation characteristics. Unexpectedly, R_S variability was lower in forests than in grasslands, ranging from 1.3-6.5 versus 3.4-12.7 μmol CO₂ m^-1 s^-1, respectively. Spatial variability of R_S in forests was related to microbial functioning through chitinase activity (50% explained variance), whereas in grasslands it was related to vegetation structure, namely graminoid abundance (27% explained variance). Apparently, the chitinase dependence of R_S variability in forests may be related to soil N limitation. This was confirmed by low N content and high C:N ratio compared to grassland soils. The greater sensitivity of grassland R_S to vegetation structure may be related to the essential root C allocation for some grasses. Thus, the first hypothesis concerning the higher spatial variability of R_S in forests than in grasslands was not confirmed, whereas the second hypothesis concerning the crucial role of soil microorganisms in forests and vegetation in grasslands as drivers of R_S spatial variability was confirmed.

Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism

Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.

Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming

Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using ¹⁸O-labeled water, from which taxon-specific rates of ¹⁸O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.

Knowns and unknowns of the soil fungal necrobiome

Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.