Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth system models

Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes

Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

Soil pore characteristics and the fate of new switchgrass-derived carbon in switchgrass and prairie bioenergy cropping systems

Monoculture switchgrass and restored prairie are promising perennial feedstock sources for bioenergy production on the lands unsuitable for conventional agriculture. Such lands often display contrasting topography that influences soil characteristics and interactions between plant growth and soil C gains. This study aimed at elucidating the influences of topography and plant systems on the fate of C originated from switchgrass plants and on its relationships with soil pore characteristics. For that, switchgrass plants were grown in intact soil cores collected from two contrasting topographies, namely steep slopes and topographical depressions, in the fields in multi-year monoculture switchgrass and restored prairie vegetation. The 13C pulse labeling allowed tracing the C of switchgrass origin, which X-ray computed micro-tomography enabled in-detail characterization of soil pore structure. In eroded slopes, the differences between the monoculture switchgrass and prairie in terms of total and microbial biomass C were greater than those in topographical depressions. While new switchgrass increased the CO2 emission in depressions, it did not significantly affect the CO2 emission in slopes. Pores of 18-90 µm Ø facilitated the accumulation of new C in soil, while > 150 µm Ø pores enhanced the mineralization of the new C. These findings suggest that polyculture prairie located in slopes can be particularly beneficial in facilitating soil C accrual and reduce C losses as CO2.

Role of genes encoding microbial carbohydrate-active enzymes in the accumulation and dynamics of organic carbon in subtropical forest soils

Microbial anabolism and catabolism regulate the accumulation and dynamics of soil organic carbon (SOC). However, very little attention has been paid to the role of microbial functional traits in the accumulation and dynamics of SOC in forest soils. In this study, nine forest soils were selected at three altitudes (600 m, 1200 m, and 1500 m) and three soil depths (0-15 cm, 15-30 cm, and 30-45 cm) located in Jiugong Mountain. Vertical traits of functional genes encoding microbial carbohydrate-active enzymes (CAZymes) were observed using metagenomic sequencing. Soil amino sugars were used as biomarkers to indicate microbial residue carbon (MRC). The results showed that GH1 (β-glucosidase: 147.49 TPM) and GH3 (β-glucosidase: 109.09 TPM) were the dominant genes for plant residue decomposition, and their abundance increased with soil depth and peaked in the deep soil at 600 m (GH1: 147.89 TPM; GH3: 109.59 TPM). The highest abundance of CAZymes for fungal and bacterial residue decomposition were GH18 (chitinase: 30.81 TPM) and GH23 (lysozyme: 58.02 TPM), respectively. The abundance of GH18 increased with soil depth, while GH23 showed the opposite trend. Moreover, MRC accumulation was significantly positively correlated with CAZymes involved in the degradation of hemicellulose (r = 0.577, p = 0.002). Compared with the soil before incubation, MRC in the topsoil at the low and middle altitudes after incubation increased by 4 % and 8 %, respectively, while MRC in the soils at 1500 m tended to decrease (p > 0.05). The mineralization capacity of SOC at 1500 m was significantly higher than that at 1200 m and 600 m (p < 0.05). Our results suggested that microbial function for degrading plant residue components, especially hemicellulose and lignin, contributed greatly to SOC accumulation and dynamics. These results were vital for understanding the roles of microbial functional traits in C cycling in forest.

Mapping turnover of dissolved organic carbon in global topsoil

Dissolved organic carbon (DOC), the labile fraction of organic carbon, is a predominant substrate for microbes. Therefore, the turnover of DOC dominates microbial respiration in soils. We compiled a global dataset (1096 data points) of the turnover rates of DOC in 0-30 cm soil profiles and integrated the data with a machine learning algorithm to develop a global map of DOC turnover rate in global topsoil. The global DOC turnover rate in 0-30 cm soil was averaged as 0.0087 day-1, with a considerable variation among biomes. The fastest DOC turnover rate was found in tropical forests (0.0175 day-1) and the lowest in tundra (0.0036 day-1), exhibiting a declining trend from low to high latitudes. The DOC turnover rate is primarily controlled by edaphic and climate factors, as confirmed by the analyses with the structural equation model and the Mental's test. With a machine learning algorithm, we produced global maps of DOC turnover rate at a monthly scale, which were further combined with a global dataset of DOC density to produce monthly maps of carbon mineralization from DOC turnover in topsoil. The annual carbon release from DOC was estimated as 27.98 Pg C year-1 from topsoil across the globe, with the largest contribution from forest biomes, followed by pasture and grassland. Tundra released the least carbon from DOC due to its low turnover rate suppressed by low temperatures. The biome- and global-scale information of DOC turnover rate and carbon release from DOC provide a benchmark for ecosystem models to better project soil carbon dynamics and their contributions to global carbon cycling in the changing environment.

Climate plays a dominant role over land management in governing soil carbon dynamics in North Western Himalayas

The soil carbon (C) dynamics is strongly influenced by climate and land-use patterns in the Himalayas. Therefore, soils under five prominent land use [e.g., maize (Zea mays), horticulture, natural forest, grassland, and wasteland] were sampled down up to 30 cm depth under two climatic conditions viz., temperate and subtropical to assess the impacts of climate and landuse on soil C dynamics. Results demonstrated that irrespective of land use, temperate soil contains 30.66% higher C than subtropical soils. Temperate soils under natural forests had the higher total organic carbon (TOC, 21.90 g kg^-1), Walkley-Black carbon (WBC, 16.42 g kg^-1), contents, and stocks (TOC, 66.92 Mg ha^-1 and WBC, 50.24 Mg ha^-1), and total soil organic matter (TSOM, 3.78%) concentration as compared to other land uses like maize, horticulture, grassland, and wasteland. Under both climatic conditions, maize land use had the lowest TOC 9.63, 6.55 g kg^-1 and WBC 7.22, 4.91 g kg^-1 at 0-15 and 15-30 cm soil depth, respectively. Horticulture land use had 62.58 and 62.61% higher TOC and WBC over maize-based land use under subtropical and temperate climatic conditions at 0-30 cm soil depth, respectively. However, soils of maize land use under temperate conditions had ∼2 times more TOC than in subtropical conditions. The study inferred that the C-losses is more in the subtropical soil than in temperate soils. Hence, the subtropical region needs more rigorous adoption of C conservation farming practices than the temperate climatic setting. Although, the adoption of C storing and conserving practices is crucial under both climatic settings to arrest land degradation. Horticultural land uses along with conservation effective soil management practices may be encouraged to restore more soil C and to improve the livelihood security of the hill populace in the North Western Himalayas.

Plant colonization mediates the microbial community dynamics in glacier forelands of the Tibetan Plateau

It has long been recognized that pH mediates community structure changes in glacier foreland soils. Here, we showed that pH changes resulted from plant colonization. Plant colonization reduced pH and increased soil organic carbon, which increased bacterial diversity, changed the community structure of both bacteria and fungi, enhanced environmental filtering, and improved microbial network disturbance resistance.

Microbial community diversity and function analysis of Aconitum carmichaelii Debeaux in rhizosphere soil of farmlands in Southwest China

Understanding how microbial communities affect plant growth is crucial for sustainable productivity and ecological health. However, in contrast with the crop system, there is limited information on the microbial community associated with the medicinal plant. We observed that altitude was the most influential factor on the soil microbial community structures of Aconitum carmichaelii Debeaux. For community composition, bacterial reads were assigned to 48 phyla, with Proteobacteria, Acidobacteriota, and Actinobacteriota being the dominant phyla. The fungal reads were assigned to seven phyla, and Ascomycota was the predominant phylum detected in most groups. The four dominant phyla were categorized as keystone taxa in the co-occurrence networks, suggesting that they may be involved in soil disease suppression and nutrient mobility. Bacterial co-occurrence networks had fewer edges, lower average degree, and lower density at YL1, HQ1, HQ2, BC, and DL than fungal networks, creating less intricate rhizosphere network patterns. Furthermore, the bacterial and fungal communities showed strong distance decay of similarity across the sampling range. Overall, this study improves our understanding of regulating rhizosphere microbial communities in soil systems and also provides potential production strategies for planting A. carmichaelii.

Polyethylene microplastic and biochar interactively affect the global warming potential of soil greenhouse gas emissions

Emerging microplastic pollution and biochar application result in their coexistence in the soil. In this study, a polyethylene microplastic, a straw biochar, and a manure biochar were applied alone or in combination to an agricultural soil to explore their interactive effects on microbial biomass carbon and nitrogen, bacterial community composition, structure and function, and the resultant greenhouse gas emissions in a 45-day laboratory incubation. At the end of incubation, the co-application of microplastic and biochar suppressed the global warming potential of cumulative greenhouse gas emissions compared with the sum of their application alone. Specifically, coexisting with microplastics increased N₂O emissions by 37.5% but decreased CH₄ emissions by 35.8% in the straw biochar added soil, and decreased N₂O, CO₂ and CH₄ emissions by 24.8, 6.2, and 65.2%, respectively, in the manure biochar added soil. A correlation network analysis illustrated that the increased global warming potential was related to the changed bacterial function and microbial biomass carbon and nitrogen in the treatments with straw biochar and/or polyethylene microplastic added, and by the changed bacterial community structure and function in the treatments with manure biochar and/or polyethylene microplastic added. Bacterial functions associated with tricarboxylic acid cycle contributed to CO₂ emissions. Bacterial functions associated with the nitrogen cycle such as nosZ and AOBamoABC were negatively and positively correlated with N₂O emissions, respectively. The interaction between different types of microplastics and soil amendments and the resultant effects on ecosystem function deserve further research.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Extreme wet precipitation and mowing stimulate soil respiration in the Eurasian meadow steppe

The imbalance of terrestrial carbon (C) inputs versus losses to extreme precipitation can have consequences for ecosystem carbon balances. However, the current understanding of how ecosystem processes will respond to predicted extreme dry and wet years is limited. The current study was conducted for three years field experiment to examine the effects of environmental variables and soil microbes on soil respiration (Rs), autotrophic respiration (Ra) and heterotrophic respiration (Rh) under extreme wet and dry conditions in mowed and unmowed grassland of Inner Mongolia. Across treatments (i.e. control, dry spring, wet spring, dry summer and wet summer), the mean of Rs was increased by 24.9 % and 24.1 % in the wet spring and wet summer precipitation treatments, respectively in mowed grassland. In other hand, the mean of Rs was decreased by -22.1 % and -3.5 % in dry spring and dry summer precipitation treatments, respectively in mowed grassland. The relative contribution of Rh and Ra to Rs showed a significant (p < 0.05) change among simulated precipitation treatments with the highest value (76.18 %) in wet summer and 26.41 % in dry summer, respectively under mowed grassland. Rs was significantly (p < 0.05) affected by the interactive effect of extreme precipitation and mowing treatments in 2020 and 2021. The effects of precipitation change via these biotic and abiotic factors explained by 52 % and 81 % in Ra and Rh, respectively in mowed grassland. The changes in microbial biomass carbon (MBC) and nitrogen (MBN) had significant (p < 0.05) direct effects on Rh in both mowed and unmowed grasslands. The influence of biotic and abiotic factors on Rs was stronger in mowed grasslands with higher standardized regression weights than in unmowed grassland (0.78 vs. 0.69). These findings highlight the importance of incorporating extreme precipitation events and mowing in regulating the responses of C cycling to global change in the semiarid Eurasian meadow steppe.

Latitudinal shifts of soil microbial biomass seasonality

Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.

Temperature Sensitivity of Topsoil Organic Matter Decomposition Does Not Depend on Vegetation Types in Mountains

Rising air temperatures caused by global warming affects microbial decomposition rate of soil organic matter (SOM). The temperature sensitivity of SOM decomposition (Q₁₀) may depend on SOM quality determined by vegetation type. In this study, we selected a long transect (3.6 km) across the five ecosystems and short transects (0.1 km) from grazed and ungrazed meadows to forests in the Northwest Caucasus to consider different patterns in Q₁₀ changes at shift of the vegetation belts. It is hypothesized that Q₁₀ will increase along altitudinal gradient in line with recalcitrance of SOM according to kinetics-based theory. The indicators of SOM quality (BR:C, respiration per unit of soil C; MBC:C, ratio of microbial biomass carbon to soil carbon; soil C:N ratio) were used for checking the hypothesis. It was shown that Q₁₀ did not differ across vegetation types within long and short transects, regardless differences in projective cover (14-99%) and vegetation species richness (6-12 units per plot). However, Q₁₀ value differed between the long and short transects by almost two times (on average 2.4 vs. 1.4). Such a difference was explained by environmental characteristics linked with terrain position (slope steepness, microclimate, and land forms). The Q₁₀ changes across studied slopes were driven by BR:C for meadows (R² = 0.64; negative relationship) and pH value for forests (R² = 0.80; positive relationship). Thus, proxy of SOM quality explained Q₁₀ variability only across mountain meadows, whereas for forests, soil acidity was the main driver of microbial activity.

An overlooked mechanism underlying the attenuated temperature response of soil heterotrophic respiration

Biogeochemical reactions occurring in soil pore space underpin gaseous emissions measured at macroscopic scales but are difficult to quantify due to their complexity and heterogeneity. We develop a volumetric-average method to calculate aerobic respiration rates analytically from soil with microscopic soil structure represented explicitly. Soil water content in the model is the result of the volumetric-average of the microscopic processes, and it is nonlinearly coupled with temperature and other factors. Since many biogeochemical reactions are driven by oxygen (O₂) which must overcome various resistances before reaching reactive microsites from the atmosphere, the volumetric-average results in negative feedback between temperature and soil respiration, with the magnitude of the feedback increasing with soil water content and substrate quality. Comparisons with various experiments show the model reproduces the variation of carbon dioxide emission from soils under different water content and temperature gradients, indicating that it captures the key microscopic processes underpinning soil respiration. We show that alongside thermal microbial adaptation, substrate heterogeneity and microbial turnover and carbon use efficiency, O₂ dissolution and diffusion in water associated with soil pore space is another key explanation for the attenuated temperature response of soil respiration and should be considered in developing soil organic carbon models.

Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition

Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH₄, CO₂, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N₂O and H₂S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO₂ emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH₄ and N₂O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N₂ fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.

Integrating McGill Wetland Model (MWM) with peat cohort tracking and microbial controls

Peatlands store a large amount of organic carbon and are vulnerable to climate change and human disturbances. However, ecosystem-scale peatland models often do not explicitly simulate the decrease in peat substrate quality, i.e., decomposability or the dynamics of decomposers during peat decomposition, which are key controls in determining peat carbon's response to a changing environment. In this paper, we incorporated the tracking of each year's litter input (a cohort) and controls of microbial processes into the McGill Wetland Model (MWMmic) to address this discrepancy. Three major modifications were made: (1) the simple acrotelm-catotelm decomposition model in MWM was changed into a time-aggregated cohort model, to track the decrease in peat quality with decomposition age; (2) microbial dynamics: growth, respiration and death were incorporated into the model and decomposition rates are regulated by microbial biomass; and (3) vertical and horizontal transport of the dissolved organic carbon (DOC) were added and used to regulate the growth of microbial biomass. MWMmic was evaluated against measurements from the Mer Bleue peatland, a raised ombrotrophic bog located in southern Ontario, Canada. The model was able to replicate microbial and DOC dynamics, while at the same time reproduce the ecosystem-level CO₂ and DOC fluxes. Sensitivity analysis with MWMmic showed increased peatland resilience to perturbations compared to the original MWM, because of the tracking of peat substrate quality. The analysis revealed the most important parameters in the model to be microbial carbon use efficiency (CUE) and turnover rate. Simulated microbial adaptation with those two physiological parameters less sensitive to disturbances leads to a significantly larger peat C loss in response to warming and water table drawdown. Thus, the rarely explored peatland microbial physiological traits merit further research. This work paves the way for further model development to examine important microbial controls on peatland's biogeochemical cycling.

Mapping soil microbial residence time at the global scale

Soil microbes are the fundamental engine for carbon (C) cycling. Microbial residence time (MRT) therefore determines the mineralization of soil organic C, releasing C as heterotrophic respiration and contributing substantially to the C efflux in terrestrial ecosystems. We took use of a comprehensive dataset (2627 data points) and calculated the MRT based on the basal respiration and microbial biomass C. Large variations in MRT were found among biomes, with the largest MRT in boreal forests and grasslands and smallest in natural wetlands. Biogeographic patterns of MRT were found along climate variables (temperature and precipitation), vegetation variables (root C density and net primary productivity), and edaphic factors (soil texture, pH, topsoil porosity, soil C, and total nitrogen). Among environmental factors, edaphic properties dominate the MRT variations. We further mapped the MRT at the global scale with an empirical model. The simulated and observed MRT were highly consistent at plot- (R² = .86), site- (R²  = .88), and biome- (R²  = .99) levels. The global average of MRT was estimated to be 38 (±5) days. A clear latitudinal biogeographic pattern was found for MRT with lower values in tropical regions and higher values in the Arctic. The biome- and global-level estimates of MRT serve as valuable data for parameterizing and benchmarking microbial models.

Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review

Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.

Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions

Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO₂ , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO₂ , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.

Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling

Global plant sulphur (S) deficiency is increasing because of a reduction in sulphate-based fertiliser application combined with continuous S withdrawal during harvest. Here, we applied ¹³C, ¹⁵N, ¹⁴C, and ³⁵S quad labelling of the S-containing amino acids cysteine (Cys) and methionine (Met) to understand S cycling and microbial S transformations in the soil. The soil microorganisms absorbed the applied Cys and Met within minutes and released SO₄^2- within hours. The SO₄^2- was reutilised by the MB within days. The initial microbial utilisation and SO₄^2- release were determined by amino acid structure. Met released 2.5-fold less SO₄^2- than Cys. The microbial biomass retained comparatively more C and S from Met than Cys. The microorganisms decomposed Cys to pyruvate and H₂S whereas they converted Met to α-ketobutyrate and S-CH₃. The microbial stoichiometries of C, N, and S derived from Cys and Met were balanced after 4 d by Cys-derived SO₄^2- uptake and Met-derived CO₂ release. The microbial C:N:S ratio dynamics showed rapid C utilisation and loss, stable N levels, and S accumulation. Thus, short-term organic S utilisation by soil microorganisms is determined by amino acid structure whilst long-term organic S utilisation by soil microorganisms is determined by microbially controlled stoichiometry.

Decreased Soil Organic Carbon under Litter Input in Three Subalpine Forests

Soil organic carbon (SOC) is the largest terrestrial organic carbon pool. Plant litter is an important source of SOC, but the knowledge gap between SOC fractions and plant litter input remains inconsistent. Here, a litter input control experiment was conducted at three subalpine forest types (coniferous forest, mixed forest, and broadleaved forest). We assessed the variations of total organic C, active organic C (easily oxidizable C, labile organic C), recalcitrant organic C, and microbial biomass C under litter input or removal. The results showed that soil total organic C decreased greatly under litter input. It was mainly caused by the change of easily oxidizable C and labile C, while the influence of recalcitrant C was small. At the same time, this effect varied among different forest types. Among them, the effect of litter input on SOC was weak and slow in the coniferous forest with low-quality litter input, while a quick effect was observed in the mixed and broadleaved forests with high-quality litter input. Microbial biomass C declined under litter input in most cases, and its variation was strongly controlled by soil temperature and freeze-thaw events. Overall, our results provide new evidence that forest type would strongly control SOC dynamics, in concert with litter quality shifts, with potential consequences for long-term C sequestration. We highlighted that litter input could reduce microbial biomass carbon which might limit the native SOC decomposition, but the loss of active C ultimately changed the SOC in the subalpine forests. It suggested that the interaction of multiple mechanisms should be considered in the study of SOC in this region.

Microbial seasonality promotes soil respiratory carbon emission in natural ecosystems: A modeling study

Seasonality is a key feature of the biosphere and the seasonal dynamics of soil carbon (C) emissions represent a fundamental mechanism regulating the terrestrial-climate interaction. We applied a microbial explicit model-CLM-Microbe-to evaluate the impacts of microbial seasonality on soil C cycling in terrestrial ecosystems. The CLM-Microbe model was validated in simulating belowground respiratory fluxes, that is, microbial respiration, root respiration, and soil respiration at the site level. On average, the CLM-Microbe model explained 72% (n = 19, p < 0.0001), 65% (n = 19, p < 0.0001), and 71% (n = 18, p < 0.0001) of the variation in microbial respiration, root respiration, and soil respiration, respectively. We then compared the model simulations of soil respiratory fluxes and soil organic C content in top 1 m between the CLM-Microbe model with (CLM-Microbe) and without (CLM-Microbe_wos) seasonal dynamics of soil microbial biomass in natural biomes. Removing soil microbial seasonality reduced model performance in simulating microbial respiration and soil respiration, but led to slight differences in simulating root respiration. Compared with the CLM-Microbe, the CLM-Microbe_wos underestimated the annual flux of microbial respiration by 0.6%-32% and annual flux of soil respiration by 0.4%-29% in natural biomes. Correspondingly, the CLM-Microbe_wos estimated higher soil organic C content in top 1 m (0.2%-7%) except for the sites in Arctic and boreal regions. Our findings suggest that soil microbial seasonality enhances soil respiratory C emissions, leading to a decline in SOC storage. An explicit representation of soil microbial seasonality represents a critical improvement for projecting soil C decomposition and reducing the uncertainties in global C cycle projection under the changing climate.

Highly decomposed organic carbon mediates the assembly of soil communities with traits for the biodegradation of chlorinated pollutants

To improve biodegradation strategies for chlorinated pollutants, the roles of soil organic matter and microbial function need to be clarified. It was hypothesised that microbial degradation of specific organic fractions in soils enhance community metabolic capability to degrade chlorinated pollutants. This field study used historic records of dieldrin concentrations since 1988 and established relationships between dieldrin dissipation and soil carbon fractions together with bacterial and fungal diversity in surface soils of Kurosol and Chromosol. Sparse partial least squares analysis linked dieldrin dissipation to metabolic activities associated with the highly decomposed carbon fraction. Dieldrin dissipation, after three decades of natural attenuation, was associated with increased bacterial species fitness for the decomposition of recalcitrant carbon substrates including synthetic chlorinated pollutants. These metabolic capabilities were linked to the decomposed carbon fraction, an important driver for the microbial community and function. Common bacterial traits among taxonomic groups enriched in samples with high dieldrin dissipation included their slow growth, large genome and complex metabolism which supported the notion that metabolic strategies for dieldrin degradation evolved in an energy-low soil environment. The findings provide new perspectives for bioremediation strategies and suggest that soil management should aim at stimulating metabolism at the decomposed, fine carbon fraction.

Untargeted Exometabolomics Provides a Powerful Approach to Investigate Biogeochemical Hotspots with Vegetation and Polygon Type in Arctic Tundra Soils

Rising temperatures in the Arctic have led to the thawing of tundra soils, which is rapidly changing terrain, hydrology, and plant and microbial communities, causing hotspots of biogeochemical activity across the landscape. Despite this, little is known about how nutrient-rich low molecular weight dissolved organic matter (LMW DOM) varies within and across tundra ecosystems. Using a high-resolution nano-liquid chromatography-mass spectrometry (LC/MS) approach, we characterized the composition and availability of LMW DOM from high-centered polygons (HCP) and low-centered polygons (LCP) with Eriophorum angustifolium or Carex aquatilis as the dominant vegetation. Over 3000 unique features (i.e., discrete mass/charge ions) were detected; 521 were identified as differentially abundant between polygonal types and 217 were putatively annotated using high mass accuracy MS data. While polygon type was a strong predictor of LMW DOM composition and availability, vegetation and soil depth were also important drivers. Extensive evidence was found for enhanced microbial processing at the LCP sites, which were dominated by Carex plant species. We detected significant differences between polygon types with varying aboveground landscape features or properties, and hotspots of biogeochemical activity, indicating LMW DOM, as quantified by untargeted exometabolomics, provides a window into the dynamic complex interactions between landscape topography, vegetation, and organic matter cycling in Arctic polygonal tundra soils.

Dynamics in Stoichiometric Traits and Carbon, Nitrogen, and Phosphorus Pools across Three Different-Aged Picea asperata Mast. Plantations on the Eastern Tibet Plateau

Understanding the variations in soil and plants with stand aging is important for improving management measures to promote the sustainable development of plantations. However, few studies have been conducted on the dynamics of stoichiometric traits and carbon (C), nitrogen (N), and phosphorus (P) pools across Picea asperata Mast plantations of different ages in subalpine regions. In the present study, we examined the stoichiometric traits and C, N, and P stocks in different components of three different aged (22-, 32-, and 42-year-old) P. asperata plantations by plot-level inventories. We hypothesized that the stoichiometric traits in mineral soil could shape the corresponding stoichiometric traits in soil microbes, tree roots and foliage, and the C, N, and P stocks of the total P. asperata plantation ecosystem would increase with increasing stand age. Our results show that the N:P ratio in mineral soil was significantly correlated with that in tree foliage and herbs. Additionally, the C:N ratio and C:P ratio in mineral soil only correlated with the corresponding stoichiometric traits in soil microbes and forest floor, respectively. Both the fractions of microbial biomass C in soil organic C and microbial biomass N in soil total N decreased with increasing stand age. The C, N, and P stocks of the total ecosystem did not continuously increase across stand development. In particular, the P stock of the total ecosystem exhibited a trend of increasing first and then decreasing. The aboveground tree biomass C accounted for more than 55% of the total ecosystem C stock regardless of stand age. In contrast, mineral soil and forest floor were the major contributors to the total ecosystem N and P stocks in all stands. This study suggested that all three different stands were N limited, and the stoichiometric homeostasis in the roots of P. asperata was more stable than that in the foliage. In addition, the soil microbial community assembly may change with increasing stand age for P. asperata plantations in the subalpine region.

Soil Microbial Community and Its Interaction with Soil Carbon Dynamics Following a Wetland Drying Process in Mu Us Sandy Land

Increasing drought globally is a severe threat to fragile desert wetland ecosystem. It is of significance to study the effects of wetland drying on microbial regulation of soil carbon (C) in the desert. In this study, we examined the impacts of wetland drying on microbial biomass, microbial community (bacteria, fungi) and microbial activity [basal microbial respiration, microbial metabolic quotient (qCO₂)]. Relationships of microbial properties with biotic factors [litter, soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP)], abiotic factors (soil moisture, pH and clay content) and biological processes (basal microbial respiration, qCO₂) were also developed. Results showed that the drying of wetland led to a decrease of soil microbial biomass carbon (MBC) content, microbial biomass nitrogen (MBN) content and fungi and bacterial abundance, and an increase of the fungi:bacteria ratio. Wetland drying also led to increased soil basal respiration and increased qCO₂, which was attributed to lower soil clay content and litter N concentration. The MBC:SOC ratios were higher under drier soil conditions than under virgin wetland, which was attributed to stronger C conserve ability of fungi than bacteria. The wetland drying process exacerbated soil C loss by strengthening heterotrophic respiration; however, the exact effects of soil microbial community structure on microbial C mineralization were not clear in this study and need further research.

Increasing microbial carbon use efficiency with warming predicts soil heterotrophic respiration globally

The degree to which climate warming will stimulate soil organic carbon (SOC) losses via heterotrophic respiration remains uncertain, in part because different or even opposite microbial physiology and temperature relationships have been proposed in SOC models. We incorporated competing microbial carbon use efficiency (CUE)-mean annual temperature (MAT) and enzyme kinetic-MAT relationships into SOC models, and compared the simulated mass-specific soil heterotrophic respiration rates with multiple published datasets of measured respiration. The measured data included 110 dryland soils globally distributed and two continental to global-scale cross-biome datasets. Model-data comparisons suggested that a positive CUE-MAT relationship best predicts the measured mass-specific soil heterotrophic respiration rates in soils distributed globally. These results are robust when considering models of increasing complexity and competing mechanisms driving soil heterotrophic respiration-MAT relationships (e.g., carbon substrate availability). Our findings suggest that a warmer climate selects for microbial communities with higher CUE, as opposed to the often hypothesized reductions in CUE by warming based on soil laboratory assays. Our results help to build the impetus for, and confidence in, including microbial mechanisms in soil biogeochemical models used to forecast changes in global soil carbon stocks in response to warming.

Microbial and abiotic controls on mineral-associated organic matter in soil profiles along an ecosystem gradient

Formation of mineral-organic associations is a key process in the global carbon cycle. Recent concepts propose litter quality-controlled microbial assimilation and direct sorption processes as main factors in transferring carbon from plant litter into mineral-organic associations. We explored the pathways of the formation of mineral-associated organic matter (MOM) in soil profiles along a 120-ky ecosystem gradient that developed under humid climate from the retreating Franz Josef Glacier in New Zealand. We determined the stocks of particulate and mineral-associated carbon, the isotope signature and microbial decomposability of organic matter, and plant and microbial biomarkers (lignin phenols, amino sugars and acids) in MOM. Results revealed that litter quality had little effect on the accumulation of mineral-associated carbon and that plant-derived carbon bypassed microbial assimilation at all soil depths. Seemingly, MOM forms by sorption of microbial as well as plant-derived compounds to minerals. The MOM in carbon-saturated topsoil was characterized by the steady exchange of older for recent carbon, while subsoil MOM arises from retention of organic matter transported with percolating water. Overall, MOM formation is not monocausal but involves various mechanisms and processes, with reactive minerals being effective filters capable of erasing chemical differences in organic matter inputs.

Aridity thresholds of soil microbial metabolic indices along a 3,200 km transect across arid and semi-arid regions in Northern China

Soil microbial processes are crucial for understanding the ecological functions of arid and semi-arid lands which occupy approximately 40% of the global terrestrial ecosystems. However, how soil microbial metabolic activities may change across a wide aridity gradient in drylands remains unclear. Here, we investigated three soil microbial metabolic indices (soil organic carbon (SOC)-based microbial respiration, metabolic quotient, and microbial biomass as a proportion of total SOC) and the degree of carbon limitation for microbial respiration along a 3,200 km transect with a wide aridity gradient. The aridity gradient was customarily expressed using the aridity index (AI) which was calculated as the ratio of mean annual precipitation to mean annual evaporation, therefore, a lower AI value indicated a higher degree of aridity. Our results showed non-linear relationships between AI values and the metabolic indices with a clear aridity threshold for each of the three metabolic indices along the aridity gradient, respectively (AI = 0.13 for basal respiration, AI = 0.17 for metabolic quotient, and AI = 0.17 for MBC:SOC ratio). These metabolic indices linearly declined when AI was above the thresholds, but did not show any clear patterns when AI was below the thresholds. We also found that soil microbial respiration was highly limited by available carbon substrates at locations with higher primary production and relatively lower level of water limitation when AI was above the threshold, a counter-intuitive pattern that microbes were more starved in ecosystems with more substrate input. However, the increasing level of carbon limitation did correspond to the declining trend of the three metabolic indices along the AI gradient, which indicates that the carbon limitation influences microbial metabolism. We also found that the ratio of microbial biomass carbon to SOC in arid regions (AI < 0.2) with extremely low precipitation and primary production were not quantitatively related to SOC content. Overall, our results imply that microbial metabolism is distinctively different in arid lands than in non-arid lands.

Global variation of soil microbial carbon-use efficiency in relation to growth temperature and substrate supply

Soil microbial carbon-use efficiency (CUE), which is defined as the ratio of growth over C uptake, is commonly assumed as a constant or estimated by a temperature-dependent function in current microbial-explicit soil carbon (C) models. The temperature-dependent function (i.e., CUE = CUE₀ + m × (T − 20)) simulates the dynamic CUE based on the specific CUE at a given reference temperature (i.e., CUE₀) and a temperature response coefficient (i.e., m). Here, based on 780 observations from 98 sites, we showed a divergent spatial distribution of the soil microbial CUE (0.5 ± 0.25; mean ± SD) at the global scale. Then, the key parameters CUE₀ and m in the above equation were estimated as 0.475 and −0.016, respectively, based on the observations with the Markov chain Monte Carlo technique. We also found a strong dependence of microbial CUE on the type of C substrate. The multiple regression analysis showed that glucose influences the variation of measured CUE associated with the environmental factors. Overall, this study confirms the global divergence of soil microbial CUE and calls for the incorporation of C substrate beside temperature in estimating the microbial CUE in different biomes.

Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions

Mycorrhizal symbioses are considered indicators of ecosystem biodiversity. However, their diversity and relevance in arid and semi-arid ecosystems are poorly understood. This study addressed this subject, the main objective being to evaluate arbuscular mycorrhizal fungi (AMF) diversity and heterogeneity in a semi-arid region. Samples of bulk and rhizosphere soil and fine roots of Medicago truncatula were collected at four different sites with the same aridity index (6.1), in Bou-Hedma National Park, Tunisia, a semi-arid ecosystem. AMF taxa were assessed by 454- pyrosequencing and identified by BLAST matching of operational taxonomic units (OTUs) against the MaarjAM database, targeting AMF SSU rRNA gene diversity. Roots were the hotspots of AMF diversity (107 OTUs out of a total of 138). Of the 138 OTUs, 113 found correspondence in the MaarjAM database, with 32 AMF virtual taxa (VTX),19 Site-exclusive (SE) and 13 common to at least two sites (Non-site exclusive, NSE); the remaining 25 OTUs grouped in 16 putative new AMF taxa (pNTX), each one consisting of OTUs sharing pairwise distances not higher than 3%. We found a high diversity and heterogeneity of AMF across the four sites, which showed, in a regression analysis, significant relation to six out of the eight environmental parameters evaluated: grazing activity and soil texture, electrical conductivity, organic matter, total phosphorus and total nitrogen. AMF colonization of plants also presented significant differences among the four sites, as well as spore density, microbial biomass and several enzymatic activities (dehydrogenase, β-glucosidase and phosphatase) evaluated in rhizosphere soils. The four sites clustered in two groups in a hierarchical clustering evaluation based on their AMF diversity (total numbers of OTU, VTX and pNTX) and the parameters referred above. The crucial role of abiotic factors, other than aridity index, on AMF community composition, was evidenced by the high heterogeneity found between AMF communities across sites under identical aridity conditions.

Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone

Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C or N content only (explaining 67% vs. 42% and 37% of variation respectively), and bulk C and N did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.

A moisture function of soil heterotrophic respiration that incorporates microscale processes

Soil heterotrophic respiration (HR) is an important source of soil-to-atmosphere CO₂ flux, but its response to changes in soil water content (θ) is poorly understood. Earth system models commonly use empirical moisture functions to describe the HR–θ relationship, introducing significant uncertainty in predicting CO₂ flux from soils. Generalized, mechanistic models that address this uncertainty are thus urgently needed. Here we derive, test, and calibrate a novel moisture function, f_m, that encapsulates primary physicochemical and biological processes controlling soil HR. We validated f_m using simulation results and published experimental data, and established the quantitative relationships between parameters of f_m and measurable soil properties, which enables f_m to predict the HR–θ relationships for different soils across spatial scales. The f_m function predicted comparable HR–θ relationships with laboratory and field measurements, and may reduce the uncertainty in predicting the response of soil organic carbon stocks to climate change compared with the empirical moisture functions currently used in Earth system models.

Empirical moisture functions that describe the relationship between soil heterotrophic respiration and moisture introduce considerable uncertainty in soil CO₂ flux predictions. Here, the authors derive a process-based moisture function by incorporating mechanisms that control soil heterotrophic respiration.

Effects of temperature, soil substrate, and microbial community on carbon mineralization across three climatically contrasting forest sites

How biotic and abiotic factors influence soil carbon (C) mineralization rate (R_S) has recently emerged as one of the focal interests in ecological studies. To determine the relative effects of temperature, soil substrate and microbial community on R_s, we conducted a laboratory experiment involving reciprocal microbial inoculations of three zonal forest soils, and measured R_S over a 61‐day period at three temperatures (5, 15, and 25°C). Results show that both R_s and the cumulative emission of C (R_cum), normalized to per unit soil organic C (SOC), were significantly affected by incubation temperature, soil substrate, microbial inoculum treatment, and their interactions (p < .05). Overall, the incubation temperature had the strongest effect on the R_S; at given temperatures, soil substrate, microbial inoculum treatment, and their interaction all significantly affected both R_s (p < .001) and R_cum (p ≤ .01), but the effect of soil substrate was much stronger than others. There was no consistent pattern of thermal adaptation in microbial decomposition of SOC in the reciprocal inoculations. Moreover, when different sources of microbial inocula were introduced to the same soil substrate, the microbial community structure converged with incubation without altering the overall soil enzyme activities; when different types of soil substrate were inoculated with the same sources of microbial inocula, both the microbial community structure and soil enzyme activities diverged. Overall, temperature plays a predominant role in affecting R_s and R_cum, while soil substrate determines the mineralizable SOC under given conditions. The role of microbial community in driving SOC mineralization is weaker than that of climate and soil substrate, because soil microbial community is both affected, and adapts to, climatic factors and soil matrix.

Soil organic carbon dynamics jointly controlled by climate, carbon inputs, soil properties and soil carbon fractions

Soil organic carbon (SOC) dynamics are regulated by the complex interplay of climatic, edaphic and biotic conditions. However, the interrelation of SOC and these drivers and their potential connection networks are rarely assessed quantitatively. Using observations of SOC dynamics with detailed soil properties from 90 field trials at 28 sites under different agroecosystems across the Australian cropping regions, we investigated the direct and indirect effects of climate, soil properties, carbon (C) inputs and soil C pools (a total of 17 variables) on SOC change rate (r_C , Mg C ha^-1  yr^-1 ). Among these variables, we found that the most influential variables on r_C were the average C input amount and annual precipitation, and the total SOC stock at the beginning of the trials. Overall, C inputs (including C input amount and pasture frequency in the crop rotation system) accounted for 27% of the relative influence on r_C , followed by climate 25% (including precipitation and temperature), soil C pools 24% (including pool size and composition) and soil properties (such as cation exchange capacity, clay content, bulk density) 24%. Path analysis identified a network of intercorrelations of climate, soil properties, C inputs and soil C pools in determining r_C . The direct correlation of r_C with climate was significantly weakened if removing the effects of soil properties and C pools, and vice versa. These results reveal the relative importance of climate, soil properties, C inputs and C pools and their complex interconnections in regulating SOC dynamics. Ignorance of the impact of changes in soil properties, C pool composition and C input (quantity and quality) on SOC dynamics is likely one of the main sources of uncertainty in SOC predictions from the process-based SOC models.

Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production

The carbon use efficiency of plants (CUE_a ) and microorganisms (CUE_h ) determines rates of biomass turnover and soil carbon sequestration. We evaluated the hypothesis that CUE_a and CUE_h counterbalance at a large scale, stabilizing microbial growth (μ) as a fraction of gross primary production (GPP). Collating data from published studies, we correlated annual CUE_a , estimated from satellite imagery, with locally determined soil CUE_h for 100 globally distributed sites. Ecosystem CUE_e , the ratio of net ecosystem production (NEP) to GPP, was estimated for each site using published models. At the ecosystem scale, CUE_a and CUE_h were inversely related. At the global scale, the apparent temperature sensitivity of CUE_h with respect to mean annual temperature (MAT) was similar for organic and mineral soils (0.029°C^-1 ). CUE_a and CUE_e were inversely related to MAT, with apparent sensitivities of -0.009 and -0.032°C^-1 , respectively. These trends constrain the ratio μ : GPP (= (CUE_a  × CUE_h )/(1 - CUE_e )) with respect to MAT by counterbalancing the apparent temperature sensitivities of the component processes. At the ecosystem scale, the counterbalance is effected by modulating soil organic matter stocks. The results suggest that a μ : GPP value of c. 0.13 is a homeostatic steady state for ecosystem carbon fluxes at a large scale.

Costimulation of soil glycosidase activity and soil respiration by nitrogen addition

Unprecedented levels of nitrogen (N) have been deposited in ecosystems over the past century, which is expected to have cascading effects on microbially mediated soil respiration (SR). Extracellular enzymes play critical roles on the degradation of soil organic matter, and measurements of their activities are potentially useful indicators of SR. The links between soil extracellular enzymatic activities (EEAs) and SR under N addition, however, have not been established. We therefore conducted a meta-analysis from 62 publications to synthesize the responses of soil EEAs and SR to elevated N. Nitrogen addition significantly increased glycosidase activity (GA) by 13.0%, α-1,4-glucosidase (AG) by 19.6%, β-1,4-glucosidase (BG) by 11.1%, β-1,4-xylosidase (BX) by 21.9% and β-D-cellobiosidase (CBH) by 12.6%. Increases in GA were more evident for long duration, high rate, organic and mixed N addition (combination of organic and inorganic N addition), as well as for studies from farmland. The response ratios (RRs) of GA were positively correlated with the SR-RRs, even when evaluated individually for AG, BG, BX and CBH. This positive correlation between GA-RR and SR-RR was maintained for most types of vegetation and soil as well as for different methods of N addition. Our results provide the first evidence that GA is linked to SR under N addition over a range of ecosystems and highlight the need for further studies on the response of other soil EEAs to various global change factors and their implications for ecosystem functions.

Carbon Availability Modifies Temperature Responses of Heterotrophic Microbial Respiration, Carbon Uptake Affinity, and Stable Carbon Isotope Discrimination

Microbial transformations of organic carbon (OC) generate a large flux of CO₂ into the atmosphere and influence the C balance of terrestrial and aquatic ecosystems. Yet, inherent heterogeneity in natural environments precludes direct quantification of multiple microbial C fluxes that underlie CO₂ production. Here we used a continuous flow bioreactor coupled with a stable C isotope analyzer to determine the effects of temperature and C availability (cellobiose concentration) on C fluxes and ¹³C discrimination of a microbial population growing at steady-state in a homogeneous, well-mixed environment. We estimated C uptake affinity and C use efficiency (CUE) to characterize the physiological responses of microbes to changing environmental conditions. Temperature increased biomass-C specific respiration rate and C uptake affinity at lower C availability, but did not influence those parameters at higher C availability. CUE decreased non-linearly with increasing temperature. The non-linear, negative relationship between CUE and temperature was more pronounced under lower C availability than under relatively high C availability. We observed stable isotope fractionation between C substrate and microbial biomass C (7~12‰ depletion), and between microbial biomass and respired CO₂ (4~10‰ depletion). Microbial discrimination against ¹³C-containing cellobiose during C uptake was influenced by temperature and C availability, while discrimination during respiration was only influenced by C availability. Shifts in C uptake affinity with temperature and C availability may have modified uptake-induced ¹³C fractionation. By stressing the importance of C availability on temperature responses of microbial C fluxes, C uptake affinity, CUE, and isotopic fractionation, this study contributes to a fundamental understanding of C flow through microbes. This will help guide parameterization of microbial responses to varying temperature and C availability within Earth-system models.

Forest biogeochemistry in response to drought

Trees alter their use and allocation of nutrients in response to drought, and changes in soil nutrient cycling and trace gas flux (N2 O and CH4 ) are observed when experimental drought is imposed on forests. In extreme droughts, trees are increasingly susceptible to attack by pests and pathogens, which can lead to major changes in nutrient flux to the soil. Extreme droughts often lead to more common and more intense forest fires, causing dramatic changes in the nutrient storage and loss from forest ecosystems. Changes in the future manifestation of drought will affect carbon uptake and storage in forests, leading to feedbacks to the Earth's climate system. We must improve the recognition of drought in nature, our ability to manage our forests in the face of drought, and the parameterization of drought in earth system models for improved predictions of carbon uptake and storage in the world's forests.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils

The chemical structure of organic matter has been shown to be only marginally important for its decomposability by microorganisms. The question of why organic matter does accumulate in the face of powerful microbial degraders is thus key for understanding terrestrial carbon and nitrogen cycling. Here we demonstrate, based on an individual-based microbial community model, that social dynamics among microbes producing extracellular enzymes (‘decomposers') and microbes exploiting the catalytic activities of others (‘cheaters') regulate organic matter turnover. We show that the presence of cheaters increases nitrogen retention and organic matter build-up by downregulating the ratio of extracellular enzymes to total microbial biomass, allowing nitrogen-rich microbial necromass to accumulate. Moreover, increasing catalytic efficiencies of enzymes are outbalanced by a strong negative feedback on enzyme producers, leading to less enzymes being produced at the community level. Our results thus reveal a possible control mechanism that may buffer soil CO₂ emissions in a future climate.

Microbial decomposers in soil provide the largest ecosystem flux of CO₂ to the atmosphere, but interactions at the microscale are poorly understood. Here, the authors use a computer modelling approach to show that social interactions among microbes buffer changing environmental conditions.

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg⁻¹ dry soil, 0.1 mmol N Kg⁻¹ dry soil, 0.1 mmol P Kg⁻¹ dry soil, and 0.1 mmol S Kg⁻¹ dry soil, respectively. These findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.

Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry

Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the application of ultrahigh resolution mass spectrometry to profile the molecular composition of SOM and its degradation during a simulated warming experiment. A soil sample, collected near Barrow, Alaska, USA, was subjected to a 40-day incubation under anoxic conditions and analyzed before and after the incubation to determine changes of SOM composition. A CHO index based on molecular C, H, and O data was utilized to codify SOM components according to their observed degradation potentials. Compounds with a CHO index score between -1 and 0 in a water-soluble fraction (WSF) demonstrated high degradation potential, with a highest shift of CHO index occurred in the N-containing group of compounds, while similar stoichiometries in a base-soluble fraction (BSF) did not. Additionally, compared with the classical H:C vs O:C van Krevelen diagram, CHO index allowed for direct visualization of the distribution of heteroatoms such as N in the identified SOM compounds. We demonstrate that CHO index is useful not only in characterizing arctic SOM at the molecular level but also enabling quantitative description of SOM degradation, thereby facilitating incorporation of the high resolution MS datasets to future mechanistic models of SOM degradation and prediction of greenhouse gas emissions.