Microbial diversity drives carbon use efficiency in a model soil

Synergies between Carbon Sequestration, Nitrogen Utilization, and Mushroom Quality: A Comprehensive Review of Substrate, Fungi, and Soil Interactions

Mushroom cultivation offers a sustainable approach by combining carbon sequestration, nitrogen use, and quality food production. This review synthesizes current knowledge on the synergistic interactions between substrate composition, fungal species, environmental factors, and their cumulative effects on the carbon and nitrogen cycles, mushroom yield, and nutritional quality. Key research gaps include the long-term impact of spent mushroom substrate (SMS) on soil carbon dynamics, limited use of fungal diversity, and the vulnerability of substrates and enzyme activity to climate change. To address these challenges, this review proposes strategies such as blending fast- and slow-decomposing agricultural waste, enriching substrates with biochar, and using genetically modified fungi to enhance lignin breakdown and stress tolerance. It also highlights promising species like Ganoderma lucidum and Trametes versicolor, and emphasizes interspecies microbial synergy. A systems-based approach combining C:N optimization, microbial interaction, and substrate innovation is recommended to improve productivity, reduce waste, and support carbon-neutral cultivation.

Microbial life-history strategies and genomic traits between pristine and cropland soils

Microbial life-history strategies [inferred from ribosomal RNA operon (rrn) gene copy numbers] and associated genomic traits and metabolism potentials in soil significantly influence ecosystem properties and functions globally. Yet, the differences in microbial strategies and traits between disturbed (cropland) and pristine soils, along with their dominant driving factors, remain underexplored. Our large-scale survey of 153 sites, including 84 croplands and 69 pristine soils, combined with long-term field experiments demonstrates that cropland soils support microbial communities with more candidate r-strategies characterized by higher rrn copy numbers and genomic traits conducive to rapid resource utilization. Conversely, pristine soils tend to host communities aligned with more candidate K-strategies marked by high resource use potentials. Elevated nitrogen (N) and phosphorus (P) levels in cropland soils emerge as key factors promoting these candidate r-strategies, overshadowing the influence of organic carbon content, soil structure, or climatic conditions. Results from four long-term field experiments also corroborate that sustained N and P inputs significantly elevate rrn copy numbers, favoring these candidate r-strategists. Our findings highlight that land use and fertilization practices critically shape microbial life-history strategies, with nutrient availability being a decisive factor in increasing the r-strategists in cropland soils.IMPORTANCEMicrobial life-history strategies and genomic traits are key determinants shaping the response of populations to environmental impacts. In this paper, 84 cropland and 69 pristine soil samples were studied, and microorganisms in two ecosystems were categorized into two types of ecological groups using the classical copiotroph-oligotroph dichotomy, promoting a general understanding of the ecological roles of microorganisms. This study is the first to investigate the microbial life-history strategies under different land uses across five climatic zones in China. The results showed that the microbes in cropland soils are more copiotrophic than pristine soils. It also demonstrates that elevated levels of nitrogen and phosphorus in cropland soils are the key factors promoting these r-strategies. This observation emphasizes the critical role of nutrient management in shaping microbial community dynamics and ecosystem functioning and lays the foundation for predicting the response of microbial community composition under resource perturbation.

A novel method for achieving ecological indicator based on vertical soil bacterial communities coupled with machine learning: A case study of a typical tropical site in China

Global industrialization has resulted in severe contamination of soil with heavy metals (HMs). Nevertheless, it is unclear if it affects the depth-resolved bacterial communities. Herein, we collected soil samples at different depths from a typical HM-contaminated site and used amplicon sequencing to determine the differences in depth-resolved bacterial communities and to assess the thresholds and ecological impacts of HMs. Results revealed that HM levels reduced markedly with soil depth. The bacteria in upper soil exhibited higher community diversity and a more complex and stable ecological network structure. As depth increased, the proportion of negative interactions gradually elevated, indicating more competitive interspecies behavior. Threshold analyses based on machine learning revealed that arsenic (As) and copper (Cu) exhibited nonlinear impacts on ecosystems. Cu demonstrated a low-threshold effect, with its ecological consequences manifested at extremely low concentrations. Our results highlighted the utility of microbial monitoring in assessing the adverse effects of HMs on soil health to support environmental management and ecological restoration.

The quality of the organic materials determines its carbon conversion efficiency in tropical latosol

Introduction

Tropical regions are characterized by high temperatures and abundant rainfall, which facilitate rapid carbon mineralization. However, research on soil organic carbon conversion efficiency (Esoc) in these areas is currently constrained by a lack of robust data support.

Methods

This study used nylon - bags with typical tropical organic materials (pineapple leaf (PAL), banana stems (BAS), coconut husk (CCH), and organic fertilizer (OF)) to explore how mixing straw with latosol impacts soil organic carbon conversion efficiency (Esoc) and products, and to understand the relationships among Esoc, material composition (glycolipid, hemicellulose, cellulose, lignin), and enzyme activity.

Results

CCH had the highest Esoc, from 37.79% to 96.87%, followed by OF with 26.71%-63.12%. The Esoc of PAL and BAS was 34.57% and 25.32% at 90 days, and 7.59% and 2.55% at 1080 days. The main factor that determines the difference in carbon conversion efficiency is the composition of organic materials. Compared with CK treatment, the soil organic carbon for PAL and BAS at 90_days was mainly O-alkyl-C, anomertic-C, and N-alkyl/methoxyl-C, with an unstable structure. The decomposition products of CCH mainly consisted of anomertic-C, aromatic-C, O-alkyl-C, carbonyl-C, and N-alkyl/methoxyl-C. The increased organic carbon in OF - mixed soil was mainly N-alkyl/methoxyl-C and anomertic-C. In the short-term (90 days), PAL, BAS, and OF increased the quantity and diversity of soil microorganisms, as well as the activities of xylosidase and cellobiohydrolase. CCH mainly enhanced soil phenol oxidase activity and maintained microbial biomass stabilityin the long-term (1080 days).

Discussion

This study revealed the changes of microbial diversity and enzyme activity under different organic materials. The promotion effects of PAL and BAS on microbial biomass, diversity and enzyme activity in the short term and the maintenance effects of CCH on the stability of microbial biomass in the later period were investigated, which provided a new basis for further exploring the function and mechanism of microorganisms in soil ecosystems.

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change.IMPORTANCEAnthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

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.

Soil Microbial Carbon Use Efficiency in Natural Terrestrial Ecosystems

Soil microbial carbon use efficiency (CUE) is the ratio of carbon allocated to microbial growth to that taken up by microorganisms. Soil microbial CUE affects terrestrial ecosystem processes such as greenhouse gas emissions, carbon turnover, and sequestration, which is an important indicator of changes in the terrestrial carbon cycle. Firstly, we summarized the three methods of soil microbial CUE, stoichiometric modeling, 13C glucose tracing, and 18O water tracing, and compared the advantages and limitations of the three methods. Then, we analyzed the single or combined effects of different environmental factors on soil microbial CUE in grassland ecosystems, forest ecosystems, and wetland ecosystems. Finally, we suggested that future research should focus on the following aspects: the influence of management patterns on CUE (such as grazing and the prohibition of grazing in grassland ecosystems, forest gap, and thinning in forest ecosystems); effects of the strategies of microorganisms for adapting to environmental changes on CUE; effects of anaerobic metabolic pathways, especially in wetland ecosystems; and effects of microbial taxonomic level. This study contributes to the investigation of the microbial mechanisms of carbon cycling in terrestrial ecosystems to mitigate the impacts of climate change.

Opposite effects of N on warming-induced changes in bacterial and fungal diversity

The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.

Nonlinear microbial thermal response and its implications for abrupt soil organic carbon responses to warming

Microbial carbon use efficiency (CUE) is a key microbial trait affecting soil organic carbon (SOC) dynamics. However, we lack a unified and predictive understanding of the mechanisms underpinning the temperature response of microbial CUE, and, thus, its impacts on SOC storage in a warming world. Here, we leverage three independent soil datasets (n = 618 for microbial CUE; n = 591 and 660 for heterotrophic respiration) at broad spatial scales to investigate the microbial thermal response and its implications for SOC responses to warming. We show a nonlinear increase and decrease of CUE and heterotrophic respiration, respectively, in response to mean annual temperature (MAT), with a thermal threshold at ≈15 °C. These nonlinear relationships are mainly associated with changes in the fungal-to-bacterial biomass ratio. Our microbial-explicit SOC model predicts significant SOC losses at MAT above ≈15 °C due to increased CUE, total microbial biomass, and heterotrophic respiration, implying a potential abrupt transition to more vulnerable SOC under climate warming.

Aerobic composting with hydrothermal carbonization aqueous phase conditioning: Stabilized active gaseous nitrogen emissions

The losses of reactive gaseous nitrogen (N), including ammonia (NH3) and nitrous oxide (N2O), represent a pressing environmental issue during composting. However, the impact of hydrothermal carbonization aqueous phase (HAP) on compost gaseous N emissions and the underlying mechanisms remain largely unexplored. Herein, Quercus acutissima leaves-derived HAP and its modified HAP (MHAP) were added to the chicken manure compost at 5 % (w/w) and 10 % (w/w) applied rates to observe changes in NH3 and N2O fluxes, compost properties and bacterial communities. Results showed that high application of HAP significantly decreased compost cumulative NH3 volatilization by 23-26 % compared to the control and MHAP. Compost NH3 and N2O emissions were significantly influenced by compost temperature and inorganic N concentrations. Moreover, HAP and MHAP at high rates reduced the relative abundance of Bacteroidota (5-29 %) and Proteobacteria (11-35 %), compared to those at low rates. Compost environmental factors and bacterial diversity were identified as dominant factors affecting gaseous N emissions, with 54 % and 25 % explanatory rates, respectively. Furthermore, high application rates of HAP are expected to reduce annual NH3 emissions from poultry manure compost by 40000 t. These findings provide insights into rational resource utilization of HAP and gaseous N emission reduction from composting.

Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome

Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures. This study developed a machine-learning approach that integrates the properties of chemical structures with the diversity of soil bacteria and functions to predict the impact of heterocyclic compounds on the microbial community and improve the design of eco-friendly heterocyclic compounds. We screened the key chemical structures of heterocyclic compounds─particularly those with topological polar surface areas (<74.2 Å2 or 111.3-154.1 Å2), carboxyl groups, and dissociation constant, which maintained high soil bacterial diversity and functions, revealing threshold effects where specific structural parameters dictated microbial responses. These eco-friendly compounds stabilize communities and increase beneficial carbon and nitrogen cycle functions. By applying these design parameters, we quantitatively assessed the eco-friendliness scores of 811 heterocyclic compounds, providing a robust foundation for guiding future applications. Our study disentangles the critical chemical structure-related properties that influence the soil microbial community and establishes a computational framework for designing eco-friendly compounds with ecological benefits from an ecological perspective.

Number of global change factors alters the relative roles of abundant and rare microbes in driving soil multifunctionality resistance

There is increasing evidence that ecosystems are affected by multiple global change factors,1,2,3 impeding the sustainability of multiple soil functions.4 Biodiversity can buffer ecosystem functions against environmental changes, a concept largely supported by insurance and portfolio theories.5,6 However, the role of soil biodiversity, especially the diversity of abundant and rare microbial taxa, in regulating soil multifunctionality resistance under an increasing number of global change factors remains poorly explored. Here, we assessed the effects of the diversity of abundant and rare microbial taxa on soil multifunctionality resistance under different numbers of global change factors using 650 microcosms. The increasing number of global change factors reduced the effects of the diversity of abundant and rare microbial taxa on soil multifunctionality resistance and shifted their relative importance. The diversity of abundant taxa showed stronger positive effects on soil multifunctionality resistance under one or two global change factors. However, the diversity of rare taxa had stronger effects under multiple co-acting global change factors. The resistance of abundant and rare microbial taxa was significantly associated with their respective diversity effects on soil multifunctionality resistance. These effects were represented by standardized slopes that evaluated the relationships between microbial diversity and multifunctionality resistance under varying numbers of global change factors. Our findings indicate a shift in the relative importance of the diversity of abundant and rare microbial taxa in regulating soil multifunctionality resistance with an increasing number of global change factors, providing new insights into the relationship between soil biodiversity and ecosystem stability under environmental disturbances.

Microbial Carbon Use Efficiency and Growth Rates in Soil: Global Patterns and Drivers

Carbon use efficiency (CUE) of microbial communities in soil quantifies the proportion of organic carbon (C) taken up by microorganisms that is allocated to growing microbial biomass as well as used for reparation of cell components. This C amount in microbial biomass is subsequently involved in microbial turnover, partly leading to microbial necromass formation, which can be further stabilized in soil. To unravel the underlying regulatory factors and spatial patterns of CUE on a large scale and across biomes (forests, grasslands, croplands), we evaluated 670 individual CUE data obtained by three commonly used approaches: (i) tracing of a substrate C by 13C (or 14C) incorporation into microbial biomass and respired CO2 (hereafter 13C-substrate), (ii) incorporation of 18O from water into DNA (18O-water), and (iii) stoichiometric modelling based on the activities of enzymes responsible for C and nitrogen (N) cycles. The global mean of microbial CUE in soil depends on the approach: 0.59 for the 13C-substrate approach, and 0.34 for the stoichiometric modelling and for the 18O-water approaches. Across biomes, microbial CUE was highest in grassland soils, followed by cropland and forest soils. A power-law relationship was identified between microbial CUE and growth rates, indicating that faster C utilization for growth corresponds to reduced C losses for maintenance and associated with mortality. Microbial growth rate increased with the content of soil organic C, total N, total phosphorus, and fungi/bacteria ratio. Our results contribute to understanding the linkage between microbial growth rates and CUE, thereby offering insights into the impacts of climate change and ecosystem disturbances on microbial physiology with consequences for C cycling.

Metabolic Flux Modeling in Marine Ecosystems

Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction networks harbored within and between the boundaries of a myriad of organisms. Gaining a quantitative understanding of how these networks operate requires mathematical tools capable of solving in silico the resource allocation problem each cell faces in real life. Toward this goal, stoichiometric modeling of metabolism, such as flux balance analysis, has emerged as a powerful computational tool for unraveling the intricacies of metabolic processes in microbes, microbial communities, and multicellular organisms. Here, we provide an overview of this approach and its applications, future prospects, and practical considerations in the context of marine sciences. We explore how flux balance analysis has been employed to study marine organisms, help elucidate nutrient cycling, and predict metabolic capabilities within diverse marine environments, and highlight future prospects for this field in advancing our knowledge of marine ecosystems and their sustainability.

Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks

The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and 18O-H2O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial-fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.

Synergistic biodegradation of trichloroethylene-contaminated soil using Typha angustifolia L. and an anaerobic degrading bacterial consortium

Plant-microorganism combined bioremediation is a highly efficient and environmentally sustainable method for the remediation of contaminated soils. Despite its potential, the synergistic effects of wetland plants and anaerobic microbial consortium on the removal of chlorinated hydrocarbons (CAHs) from soil remain inadequately understood. In this study, an anaerobic bacterial consortium, capable of completely dechlorinating trichloroethylene (TCE), was enriched and screened from long-term CAH-contaminated soil. Subsequently, the combined effects of the wetland plant Typha angustifolia L. and the anaerobic bacterial consortium on the removal of TCE from soil were investigated, along with the underlying microbial mechanisms. The results demonstrated that the anaerobic bacterial consortium was able to completely convert 0.5 mM TCE to vinyl chloride (VC) within 7 days, and subsequently degrade VC to ethylene within 48 days. The integration of Typha angustifolia L. with the anaerobic bacterial consortium significantly enhanced both the removal and complete dechlorination of TCE from the soil compared to either treatment alone. Furthermore, this combination substantially increased the diversity and richness of soil bacterial communities, enriched dechlorinating microorganisms, and elevated the relative abundance of dehalogenating enzymes and peroxidases involved in pollutant degradation. In addition, the combination resulted in a more complex soil bacterial community, closer microbial interactions, and a more stable microbial co-occurrence network. This study extends the scope of plant-microorganism combined bioremediation for CAH- contaminated soils.

Adaptive expression of phage auxiliary metabolic genes in paddy soils and their contribution toward global carbon sequestration

Habitats with intermittent flooding, such as paddy soils, are crucial reservoirs in the global carbon pool; however, the effect of phage-host interactions on the biogeochemical cycling of carbon in paddy soils remains unclear. Hence, this study applied multiomics and global datasets integrated with validation experiments to investigate phage-host community interactions and the potential of phages to impact carbon sequestration in paddy soils. The results demonstrated that paddy soil phages harbor a diverse and abundant repertoire of auxiliary metabolic genes (AMGs) associated with carbon fixation, comprising 23.7% of the identified AMGs. The successful annotation of protein structures and promoters further suggested an elevated expression potential of these genes within their bacterial hosts. Moreover, environmental stressors, such as heavy metal contamination, cause genetic variation in paddy phages and up-regulate the expression of carbon fixation AMGs, as demonstrated by the significant enrichment of related metabolites (P < 0.05). Notably, the findings indicate that lysogenic phages infecting carbon-fixing hosts increased by 10.7% under heavy metal stress. In addition, in situ isotopic labeling experiments induced by mitomycin-C revealed that by increasing heavy metal concentrations, 13CO2 emissions from the treatment with added lysogenic phage decreased by approximately 17.9%. In contrast, 13C-labeled microbial biomass carbon content increased by an average of 35.4% compared to the control. These results suggest that paddy soil phages prominently influence the global carbon cycle, particularly under global change conditions. This research enhances our understanding of phage-host cooperation in driving carbon sequestration in paddy soils amid evolving environmental conditions.

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.

Degradation-driven vegetation-soil-microbe interactions alter microbial carbon use efficiency in Moso bamboo forests

Microbial carbon utilization efficiency (CUE) is a crucial indicator for evaluating the efficiency of soil carbon sequestration and transformation, which is applied to quantify the proportion of soil carbon extracted by microbes for anabolism (growth) and catabolism (respiration). Previous studies have shown that the degradation of Moso bamboo forests (Phyllostachys edulis) destroyed the aboveground bamboo structure, reduced vegetation carbon storage, and weakened ecosystem carbon sequestration capacity. Interestingly, soil organic carbon stocks are gradually increasing. However, the mechanism by which degradation-induced changes in soil and vegetation characteristics affect microbial CUE and drive soil carbon sequestration remains unclear. Here we selected four stands with the same origin but different degradation years (intensive management, CK; 2 years' degradation, DM1; 6 years' degradation, DM2; and 10 years' degradation, DM3) based on the local management profiles. The principle of space-for-time substitution was used to investigate the changes in microbial CUE along a degradation time and to further identify the controlling biotic and abiotic factors. Our finding showed that microbial CUE increased by 12.27 %, 31.01 %, and 55.95 %, respectively, compared with CK; whereas microbial biomass turnover time decreased from 23.99 ± 1.11 to 17.16 ± 1.20 days. Promoting microbial growth was the main pathway to enhance microbial CUE. Massive inputs of vegetative carbon replenished soil carbon substrate content, and altered microbial communities and life history strategy, which in turn promoted microbial growth and increased microbial CUE. These findings provide theoretical support for the interactions between carbon dynamics and microbial physiology in degraded bamboo forests, and reinforce the importance of vegetation and microbial properties and soil carbon substrates in predicting microbial CUE.

New insights into the prediction for the potential of soil organic carbon accumulation: From the perspective of non-equilibrium statistical mechanics

The accumulation of soil organic carbon (SOC) is significant for soil health and ecosystem services. Numerous studies have assessed the dynamic changes of SOC by considering the microbial system as an equilibrium system. However, they failed to reveal the complexity of the SOC accumulation/loss process, as the microbial system is a non-equilibrium system affected by stochastic fluctuations from the external environment. This study is the first to explore the complex non-equilibrium relationship between microbial carbon use efficiency (CUE) and SOC by using potential landscape and flux in non-equilibrium statistical mechanics. Nitrogen (N) was identified as the most critical environmental factor influencing CUE on a global scale, with the transition between the carbon loss state and the carbon sequestration state observed along N gradients. Random perturbations of other environmental factors could also trigger transition. Non-equilibrium thermodynamic quantities indicated that carbon sequestration had the potential to be achieved when N = 0.5 g/kg, where active soil management measures should be taken. Furthermore, the non-equilibrium relationship between CUE and SOC was clarified through potential energy analysis, where the average deviation between predictions and actual observations of SOC is about 1.9792 g/kg. This study provides an effective framework for predicting SOC accumulation.

Carbon flow allocation patterns of CH4, CO2, and biomass production vary with sewage and sediment microbial and biochemical factors in the anaerobic sewer environment

Understanding the carbon (C) fate in municipal sewers is imperative for optimizing current sewer-C-degradation control and treatment efficiency, aligning with China's C-neutrality strategy in determining the exact C budget of the wastewater system. This study used laboratory batch tests mimicking the anaerobic sewer environment and sewage-sediment stratification to evaluate C flow allocation (CFA) patterns in response to biotic and abiotic variables. We quantified the C equivalent mass (CEM) and used absolute quantitative 16S rRNA gene amplicon sequencing to characterize the microbiome. The substantial methane production (CH4, 17.2%-18.8%) required both activated sediment and exogenous C, while biomass production (BP, 63.1%-74.9%) formed C sink predominated as the main CFA direction under the stratified state. This was supported by the high diversity, interspecific interactions, and metabolic capacity of the sediment microbiome. However, CH4 and BP patterns demonstrated non-synchronicity and opposite dynamic characteristics. Carbon dioxide (CO2, 64.0%-81.3%) production dominated the sewage CFA. The absolute abundance of the sediment microbiome, which was 5.6 times higher than that of the sewage, exhibited a strong increase in magnitude across the phases. It was primarily associated with biomass growth and N metabolism, whereas sewage showed differentiated and competing communities and appeared to act mainly as the exogenous C sources. We constructed a binary quadratic linear model revealing the non-linear relationship between ACK activity, DOC degradation rate, and CEMCH4 rate; the former maintained low CH4 production when the available substrate was insufficient. The influence of N and S factors on the CFA is complex and multi-faceted. These findings highlight the importance of further investigations into the process-based framework of the sewer C budget, focusing on the C source-emission-sink functions and mass balance.

Aridity-Driven Change in Microbial Carbon Use Efficiency and Its Linkage to Soil Carbon Storage

Global warming is generally predicted to increase aridity in drylands, while the effects of aridity changes on microbial carbon use efficiency (CUE) and its linkage to soil organic carbon (SOC) storage remain unresolved, limiting the accuracy of soil carbon dynamic predictions under changing climates. Here, by employing large-scale soil sampling from 50 sites along an ~6000 km aridity gradient in northern China, we report a significant decreasing trend in microbial CUE (ranging from approximately 0.07 to 0.59 across the aridity gradient) with increasing aridity. The negative effect of aridity on microbial CUE was further verified by an independent moisture manipulation experiment, which revealed that CUE was lower under lower moisture levels than under higher moisture levels. Aridity-induced increases in physicochemical protection or decreases in microbial diversity primarily mediated the decrease in CUE with increasing aridity. Moreover, we found a highly positive microbial CUE-SOC relationship, and incorporating CUE improved the explanatory power of SOC variations along the aridity gradient. Our findings provide empirical evidence for aridity-induced reductions in microbial CUE over a broad geographic scale and highlight that increasing aridity may be a crucial mechanism underlying SOC loss by suppressing the ability of soil microorganisms to sequester carbon.

Seasonal effects of long-term warming on ecosystem function and bacterial diversity

Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.

Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment

The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5-35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86-181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25-35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.

Fe oxides simultaneously improve stability of Cd and carbon in paddy soil：The underlying influence at aggregate level

Iron (Fe) oxides have a strong adsorption affinity for Cd and organic carbon (SOC). However, under alternate wet-dry (IF) condition,the influences of Fe oxides on the speciation and disrtribution of Cd and SOC in soil aggregates are unkown. In the present study, soils untreated (S), removed (S-Fe) or added (S+Fe) Fe oxide soils were blended with cadmium chloride solution and cultivated for 56 days under different moisture management practices. Compared with the S-Fe soil, the IF treatment increased the contents of Fe oxide-bound SOC (Fe-OC) and Fe/Mn oxide-bound Cd (Fe/Mn-Cd) by 18.5-29.8-fold and 1.45-2.45-fold, repectively, in the S and S+Fe soils, corresponding to a 36 %-42 % increase in the recalcitrant C pool (RCP) and a 53 %-87 % decrease in the exchangeable Cd content. These results could be attributed to soil particle aggregation and Fe redistribution. Fe addition promoted the transfer of Cd/SOC accumulated in microaggregates to macroaggregates and increased the variable negative charge content in macroaggregates and the adsorption capacity of macroaggregates for Cd/SOC. More Cd/SOC accumulated in macroaggregates in Fe oxide-bound form, which reduced the risk of Cd migration and Cd availability and increased the physical protection of SOC. Therefore, Fe oxide has great potential to simultaneously reduce carbon emissions and cadmium toxicity in paddy soil.

Unveiling the long-term dynamic effects: Biochar mediates bacterial communities to modulate the petroleum hydrocarbon degradation in oil-contaminated sediments

Sediment, as the destination of marine pollutants, often bears much more serious petroleum pollution than water. Biochar is increasingly utilized for remediating organic pollutant-laden sediments, yet its long-term impacts on oil-contaminated sediment remain poorly understood. In this study, simulation experiments adding 2.5 wt% biochars (corn straw and wood chips biochar at different pyrolysis temperatures) were conducted. The effects on petroleum hydrocarbon attenuation, enzyme activities, and microbial community structure were systematically investigated. Results showed enhanced degradation of long-chain alkanes in certain biochar-treated groups. Biochar species and PAH characteristics together lead to the PAHs' attenuation, with low-temperature corn straw biochar facilitating the degradation of phenanthrene, fluorene, and chrysene. Initially, biochars reduced polyphenol oxidase activity but increased urease and dehydrogenase activities. However, there was a noticeable rise in polyphenol oxidase activity for a long time. Biochars influenced bacterial community succession and abundance, likely due to nutrient release stimulating microbial activity. The structural equations model (SEM) reveals that DON affected the enzyme activity by changing the microbial community and thus regulated the degradation of PAHs. These findings shed light on biochar's role in bacterial communities and petroleum hydrocarbon degradation over extended periods, potentially enhancing biochar-based remediation for petroleum-contaminated sediments.

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils

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

Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

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

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

The Response of Rhizosphere Microbial C and N-Cycling Gene Abundance of Sand-Fixing Shrub to Stand Age Following Desert Restoration

Rhizosphere microorganisms play a pivotal role in biogeochemical cycles, particularly in relation to carbon (C) and nitrogen (N) cycles. However, the impact of stand age on the composition of rhizosphere microbial communities and the abundance involved in C and N cycling remains largely unexplored in restoration ecosystems dominated by shrubs of temperate deserts. This study focuses on revealing changes in microbial composition and functional genes in the rhizosphere soil of Caragana korshinskii after revegetation, as well as their response mechanisms to changes in environmental factors. The alpha diversity of bacteria tended to increase with stand age, whereas that of fungi decreased. The abundance of denitrification; dissimilatory nitrate reduction to ammonium, nitrification, and ammonium assimilation; and C fixation-related gene levels increased with stand age, whereas those related to the degradation of starch, pectin, hemicellulose, cellulose, and aromatics decreased. The parameters MBC, MBN, and TC were the key factors affecting the bacterial community, whereas the fungal community was regulated by TN, EC, pH, and MBC. Stand age indirectly regulated C and N cycling functions of genes through altered soil properties and microbial community structures. This study presents a novel approach to accurately evaluate the C and N cycling dynamics within ecosystems at various stages of restoration.

Core microbial taxonomies that maintain high organic carbon content in upland soil

The accumulation of soil carbon (C) is crucial for the productivity and ecological function of farmland ecosystems. The balance between microbial carbon dioxide (CO2) emission and fixation determines the sustained accumulation potential of C in soil. Microorganisms involved in this process are highly obscure, thus hindering identification and further application of microorganisms with fertile soil function. In this study, a series of typical upland farmland soils were collected from 29 regions and their microbial community structure and soil C fractions were analyzed. Additionally, the rates of CO2 emission and fixation in each soil were measured. The results showed that the correlation between soil CO2 emissions and the SOC concentration was logarithmic, while that between CO2 fixation and SOC was linear. Bacterial and fungal diversity showed an upward trend with increasing soil C, and their α diversity was significantly correlated with CO2 fixation, but not correlated with CO2 emission. Fungi were more associated with soil C than bacteria, and the strength of linkage with soil C varied among the different phyla of microorganisms. Furthermore, the core microbial taxa in soils with low, medium and high SOC levels were identified by discarding redundant amplicon sequence variants, and their community differentiation was significantly driven by soil CO2 emission and fixation based on Mantel analysis. The high abundance of Chloroflexi, Nitrospirota, Actinobacteria, and Mortierellomycota in core taxa might indicate a high level of SOC level. This study highlights that SOC fluctuations are mainly driven by the core microbial taxa, rather than all microbial taxa in the agricultural system. Our research sheds light on the targeted regulation of the soil microbial community structure in upland farmland for soil fertility enhancement.

Enhancement of microbial community dynamics and metabolism in compost through ammonifying cultures inoculation

The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%-33.87% and nitrogen metabolism annotation by 26.69%-63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices.

Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants

Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.

Prediction of As and Cd dissolution in various soils under flooding condition

Although the mobility of arsenic (As) and cadmium (Cd) in soils during the flooding-drainage process has been intensively studied, predicting their dissolution among various soils still remains a challenge. After comprehensively monitoring multiple parameters related to As and Cd dissolution in 8 soils for a 60-day anaerobic incubation, the redundancy analysis (RDA) and structural equation model (SEM) were employed to identify the key factors and influencing pathways controlling the dynamic release of As and Cd. Results showed that pH alone explained 90.5 % Cd dissolution, while the dissolved-Fe(II) and 5 M-HCl extractable Fe(II) jointly only explained 50.6 % As dissolution. After data normalization, the ratio of Fe(II) to 5 M-HCl extracted total Fe (i.e. FetotII/Fetot) significantly improved the correlation to R2 = 0.824 (p < 0.001) with a fixed slope of 0.393 among the 8 soils. Our results highlight the crucial role played by the reduction degree of total iron contents in determining both the reduction and dissolution of As during flooding. In contrast, dissolved-Fe(II) was too vulnerable to soil properties to be a stable indicator of As dissolution. Therefore, we propose to replace the dissolved-Fe(II) with this novel ratio as the key index to quantitatively assess the kinetic change of As solubility potential across various soils under flooding conditions.

Regulatory path for soil microbial communities depends on the type and dose of microplastics

To reveal the feedbacks and regulating mechanisms of microplastic types and doses on microbial community, a microcosm experiment was carried out with two non-degradable microplastics [polyethylene (PE) and polyvinyl chloride (PVC)] and four biodegradable microplastics [poly(butylene succinate) (PBS), polyhydroxyalkanoates (PHA), poly(butyleneadipate-co-terephthalate) (PBAT), and polypropylene carbonate (PPC)] at different levels (1 %, 7 %, and 28 %). As a result, the content of total carbon (TC), soil organic carbon (SOC), and microbial biomass carbon (MBC) (expect MBC in PBS soil) increased with increasing doses of microplastics, and increased at the lowest PE dose rate. Biodegradable microplastics created a more active ecological niche while enriching more pathogens than non-degradable microplastics. Structural equation modeling indicated that microbial diversities were in a type-dependent assembly, whereas microbial compositions were more profoundly affected by the microplastic doses, ultimately. The standardized total effect coefficient of microplastic types on bacterial and fungal diversities was - 0.429 and - 0.282, and that of doses on bacterial and fungal compositions was 0.487 and 0.336, respectively. Both microplastic types and doses significantly impacted pH, electrical conductivity, total nitrogen, TC, SOC, and MBC, subsequently inhibiting microbial diversities and stimulating microbial compositions with particular pathways. The results provide a comprehensive understanding for evaluating the potential risk of microplastics.

Effects of exogenous copper on microbial metabolic function and carbon use efficiency of Panax notoginseng planting soil

Soil copper (Cu) pollution is a serious environmental risk in the Panax notoginseng planting area. However, the effect of Cu on soil microbial metabolism and nutrient cycling in this area remains unknown. Therefore, Biolog ECO-plate and enzyme stoichiometry methods were utilized in this study to investigate the impact of exogenous Cu (control: 0 mg·kg-1; Cu100: 100 mg·kg-1; Cu400: 400 mg·kg-1; and Cu600: 600 mg·kg-1) on the metabolic function of soil microbial and nutrient limitation in the P. notoginseng soil. The results indicated that Cu100 significantly increased soil organic carbon (SOC), total phosphorus (TP), soil C:N, microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) 9.89%, 15.65%, 17.91%, 61.87%, and 90.56% higher than the control, respectively. Moreover, the carbon source utilization ratio of carbohydrates, amino acids, and amphiphilic compounds of Cu100 also increased by 7.16%, 25.47%, and 84.68%, respectively, compared with the control. The activities of β-1,4-glucosidase, cellobiohyrolase, leucine amino peptidase, β-1,4-N-acetylglucosaminidase, and phosphatase significantly decreased with increasing Cu concentration. Soil enzyme stoichiometry showed that all treatments were limited by nitrogen (vector angle < 45°; 19.045-22.081). Cu600 led to the lowest carbon limitation (1.798) and highest carbon use efficiency (CUE:0.267). The PLS-SEM model also showed that MBC, MBN, MBP, and microbial diversity positively affected carbon and nitrogen limitation (0.654 and 0.424). Soil carbon, nitrogen, phosphorus, stoichiometric ratio, MBC, MBN, and MBP positively affected CUE (0.527 and 0.589). The microbial diversity index significantly negatively affected CUE (-1.490). Multiple linear stepwise regression analyses showed that CUE was mainly influenced by MBC, AP, C:P, and LAP. Thus, P. notoginseng soil can benefit soil microbial carbon and nitrogen limitations at low Cu concentrations. Clarifying the metabolic activity and nutritional status of microorganisms under Cu stress can provide some theoretical basis for realizing China's comprehensive and effective management and control policies for environmental risks from metals by 2035.

Contrasting roles of plant, bacterial, and fungal diversity in soil organic carbon accrual during ecosystem restoration: A meta-analysis

Plant and microbial diversity plays vital roles in soil organic carbon (SOC) accumulation during ecosystem restoration. However, how soil microbial diversity mediates the positive effects of plant diversity on carbon accumulation during vegetation restoration remains unclear. We conducted a large-scale meta-analysis with 353 paired observations from 65 studies to examine how plant and microbial diversity changed over 0-160 years of natural restoration and its connection to SOC accrual in the topsoil (0-10 cm). Results showed that natural restoration significantly increased plant aboveground biomass (122.09 %), belowground biomass (153.05 %), and richness (21.99 %) and SOC accumulation (32.34 %) but had no significant impact on microbial diversity. Over time, bacterial and fungal richness increased and then decreased. The responses of major microbial phyla, in terms of relative abundance, varied across restoration and ecosystem types. Specifically, Ascomycota and Zygomycota decreased more under farmland abandonment than under grazing exclusion. In forest, Bacteroidetes, Ascomycota, and Zygomycota significantly decreased after natural restoration. The increase in SOC and Basidiomycota was higher in forest than in grassland. Based on standardized estimates, structural equation modeling showed that plant diversity had the highest positive effect (0.55) on SOC accrual, and while fungal diversity (0.15) also had a positive effective, bacterial diversity (-0.20) had a negative effect. Plant diversity promoted SOC accumulation by directly impacting biomass and soil moisture and total nitrogen and indirectly influencing soil microbial richness. This meta-analysis highlights the significant roles of plant diversity and microbial diversity in carbon accumulation during natural restoration and elucidates their relative contributions to carbon accumulation, thereby aiding in more precise predictions of soil carbon sequestration.

Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities

In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.

Conceptualizing soil fauna effects on labile and stabilized soil organic matter

Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems

Introduction

Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.

Methods

Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.

Results

Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%).

Conclusion

This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Microorganisms Directly Affected Sediment Carbon–Nitrogen Coupling in Two Constructed Wetlands

Clarifying the carbon–nitrogen coupling pattern in wetlands is crucial for understanding the driving mechanism of wetland carbon sequestration. However, the impacts of plants and environmental factors on the coupling of carbon–nitrogen in wetland sediments are still unclear. Sediment samples from plant (Typha angustifolia and Phragmites australis)-covered habitats and bare land were collected in two constructed wetlands in northern China. The contents of different forms of carbon and nitrogen in sediments and plants, and the sediment microbial community were detected. It was found that the sediment carbon to nitrogen (C/N) ratios did not differ significantly in the bare sites of different wetlands, but did in the plant-covered sites, which highlighted the different role of plants in shifting the carbon–nitrogen coupling in different constructed wetlands. The effects of plants on the sediment carbon–nitrogen coupling differed in two constructed wetlands, so the structural equation model was used and found that sediment microorganisms directly affected sediment C/N ratios, while water and sediment physicochemical properties indirectly affected sediment C/N ratios by altering sediment microbial functions. Multiple linear regression models showed that water pH, sediment moisture content, water dissolved oxygen, and water depth had a greater influence on the carbon metabolism potential of the sediment microbial community, while sediment moisture content had the greatest impact on the sediment microbial nitrogen metabolism potential. The study indicates that variations in environmental conditions could alter the influence of plants on the carbon and nitrogen cycles of wetland sediments. Water environmental factors mainly affect microbial carbon metabolism functions, while soil physicochemical factors, especially water content, affect microbial carbon and nitrogen metabolism functions.

Mild to moderate drought stress reinforces the role of functional microbiome in promoting growth of a dominant forage species (Neopallasia pectinata) in desert steppe

Background

Desert steppe ecosystems are prone to drought stress, which influences the ecological balance and sustainable development of grasslands. In addition to directly restrict plant growth, drought stress indirectly impacts plant fitness by altering the diversity and function of root-associated microbiomes. This begs the question of whether the functional microbiome of forage plants, represented by synthetic microbial communities (SynComs), can be leveraged to mitigate drought stress in desert steppes and promote the ecological restoration of these fragile ecosystems.

Methods

A pot experiment was conducted to evaluate the role of SynComs in improving the plant growth and drought stress resistance of Neopallasia pectinata (Pall.) Poljak in desert steppe in Inner Mongolia, China. Six SynComs were derived from the rhizosphere and root endosphere of 12 dominant forage species in the desert steppe. Each SynCom comprised two to three bacterial genera (Bacillus, Protomicromonospora, and Streptomyces). We examined the capacities of different SynComs for nutrient solubilization, phytohormone secretion, and enzymatic activity.

Results

Under no water stress (75% soil water holding capacity, WHC), single strains performed better than SynComs in promoting plant growth in terms of stem diameter, root length, and plant dry weight, with the greatest effects observed for Streptomyces coeruleorubidus ATCC 13740 (p < 0.05). However, under mild to moderate drought stress (55% and 35% WHC), SynComs outperformed single strains in enhancing plant biomass accumulation and inducing the production of resistance-related substances (p < 0.05). No significant effect of single strains and SynComs emerged under extreme drought stress (20% WHC).

Conclusion

This study underscores the potential of SynComs in facilitating forage plants to combat drought stress in desert steppe. Mild to moderate drought stress stimulates SynComs to benefit the growth of N. pectinata plants, despite a soil moisture threshold (21% WHC) exists for the microbial effect. The use of SynComs provides a promising strategy for the ecological restoration and sustainable utilization of desert steppes by manipulating the functional microbiome of forage plants.

Thinning enhances forest soil C storage by shifting the soil toward an oligotrophic condition

Forests are significant carbon reservoirs, with approximately one-third of this carbon stored in the soil. Forest thinning, a prevalent management technique, is designed to enhance timber production, preserve biodiversity, and maintain ecosystem functions. Through its influence on biotic and abiotic factors, thinning can profoundly alter soil carbon storage. Yet, the full implications of thinning on forest soil carbon reservoirs and the mechanisms underpinning these changes remain elusive. In this study, we undertook a two-year monitoring initiative, tracking changes in soil extracellular enzyme activities (EEAs), microbial communities, and other abiotic parameters across four thinning intensities within a temperate pine forest. Our results show a marked increase in soil carbon stock following thinning. However, thinning also led to decreased dissolved organic carbon (DOC) content and a reduced DOC to soil organic carbon (SOC) ratio, pointing toward a decline in soil carbon lability. Additionally, fourier transform infrared spectroscopy (FTIR) analysis revealed an augmented relative abundance of aromatic compounds after thinning. There was also a pronounced increase in absolute EEAs (per gram of dry soil) post-thinning, implying nutrient limitations for soil microbes. Concurrently, the composition of bacterial and fungal communities shifted toward oligotrophic dominance post thinning. Specific EEAs (per gram of soil organic matter) exhibit a significant reduction following thinning, indicating a deceleration in organic matter decomposition rates. In essence, our findings reveal that thinning transitions soil toward an oligotrophic state, dampening organic matter decomposition, and thus bolstering the soil carbon storage potential of forest. This study provides enhanced insights into the nuanced relationship between thinning practices and forest soil carbon dynamics, serving as a robust foundation for enlightened forest management strategies.

Soil stoichiometric imbalances constrain microbial-driven C and N dynamics in grassland

Grassland restoration leads to excessive soils with carbon (C) and nitrogen (N) contents that are inadequate to fulfill the requirements of microorganisms. The differences in the stoichiometric ratios of these elements could limit the activity of microorganisms, which ultimately affects the microbial C, N use efficiencies (CUE, NUE) and the dynamics of soil C and N. The present study was aimed at quantifying the soil microbial nutrient limitation and exploring the mechanisms underlying microbial-induced C and N dynamics in chrono-sequence of restored grasslands. It was revealed that grassland restoration increased microbial C, N content, microbial C, N uptake, and microbial CUE and NUE, while the threshold elemental ratio (the C:N ratio) decreased, which is mainly due to the synergistic effect of the microbial biomass and enzymatic stoichiometry imbalance after grassland restoration. Finally, we present a framework for the nutrient limitation strategies that stoichiometric imbalances constrain microbial-driven C and N dynamics. These results are the direct evidence of causal relations between stoichiometric ratios, microbial responses, and soil C, N cycling.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

Biodegradable Mineral Plastics

Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.

Soil organic matter degradation and methylmercury dynamics in Hg-contaminated soils: Relationships and driving factors

Biodegradation of soil organic matter (SOM), which involves greenhouse gas (GHG) emissions, plays an essential role in the global carbon cycle. Over the past few decades, this has become an important research focus, particularly in natural ecosystems. SOM biodegradation significantly affects contaminants in the environment, such as mercury (Hg) methylation, producing highly toxic methylmercury (MeHg). However, the potential link between GHG production from SOM turnover in contaminated soils and biogeochemical processes involving contaminants remains unclear. In this study, we investigated the dynamics of GHG, MeHg production, and the relationship between biogeochemical processes in soils from two typical Hg mining sites. The two contaminated soils have different pathways, explaining the significant variations in GHG and MeHg production. The divergence of the microbial communities in these two biogeochemical processes is essential. In addition to the microbial role, abiotic factors such as Hg species can significantly affect MeHg production. On the other hand, we found an inverse relationship between CH4 and MeHg, suggesting that carbon emission reduction policies and management could inadvertently increase the MeHg levels. This highlights the need for an eclectic approach to organic carbon sequestration and contaminant containment. These findings suggest that it is difficult to establish a general pattern to describe and explain the SOM degradation and MeHg production in contaminated soils within the specific scenarios. However, this study provides a case study and helpful insights for further understanding the links between environmental risks and carbon turnover in Hg mining areas.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.