● We estimated the effect of three crop strategies on soil health based on 63 functional genes in long-term fields.

Given the often-independent study of microbial diversity and function, the comprehensive impact of various cropping patterns on both aspects, as well as the interconnections between them, remains unclear. This gap constrainsus from evaluating the impact of soil microbiome shifts on soil health across varying agricultural management regimes. Here, we examined the associations between microbial diversity and soil multifunctionality in three long-term cropping patterns: continuous soybean cropping, soybean-corn rotation, and continuous corn cropping. We targeted 63 functional genes associated with carbon, nitrogen, phosphorus and sulfur cycling to assess soil multifunctionality. Our study demonstrated that the biodiversity and interactions of keystone phylotypes had significant positive associations with multiple soil functional genes, such as organic carbon degradation and fixation, nitrogen fixation and phosphorus solubilization. The analysis of retrieved complete genome revealed that the keystone bacteria identified in our study harbored these functional genes. Moreover, these keystone phylotypes showed associations with the dissipation of herbicide residues. Above all, we revealed that rotation of soybean with corn cropping enhanced a greater diversity of keystone phylotypes and thus fueled soil functions. Collectively, our results highlighted the importance of rotation with soybean in maintaining soil health, which could give a mechanism-based guidance for a sustainable agroecosystem.

● Soil respiration rates ( R _s) were measured in New Zealand dairy grassland.

Soil respiration (R_s), the CO₂ release from root respiration and microbial metabolism, affects global soil carbon storage and cycling. Only few studies have looked at R_s in the southern hemisphere, especially regarding the interaction between soil type and environmental factors on R_s in dairy grassland. We investigated the relationship between R_s and soil temperature (T_s), soil water content (SWC), soil type, and other environmental factors based on summer and winter measurements at four sites in New Zealand. Across sites, soil respiration rates ranged from 0.29 to 14.58 with a mean of 5.38 ± 0.13 (mean ± standard error) µmol CO₂ m⁻² s⁻¹. Mean summer R_s was 86.5% higher than mean winter R_s, largely driven by organic/gley and pumice soils while ultic soils showed very little seasonal temperature sensitivity. Overall mean R_s in organic/gley soils was 108.0% higher than that in ultic soils. The high R_s rate observed in organic/gley was likely due to high soil organic matter content, while low R_s in ultic and pallic soils resulted from high clay content and low hydraulic conductance. Soil temperature drove overall R_s. Our findings indicate that soil type and soil temperature together best explain R_s. This implies that a mere classification of land use type may be insufficient for global C models and should be supplemented with soil type information, at least locally.

● Biosolids boost OM mineralization, enhancing soil health.

Economic development triggers environmental pollution. To address this issue and mitigate its consequences on the environment and human health, urban wastewater treatment plants are commonly employed to produce treated water and biosolids. However, biosolid disposals pose issues due to space limits and leachate contamination. This study investigates the potential of using biosolids as an organic amendment to remediate soil contaminated with leachate from an open dump in Mexico. Treatments with different doses of biosolids were tested (control, without addition of biosolids; high, medium, and low doses, with a C/N = 8, 10, 12 respectively). The physicochemical and biological characteristics of the soil and biosolids were analyzed, and the dynamics of carbon and nitrogen mineralization over time were studied. The developed soil quality index, primarily based on the mineralized nitrogen indicator, differentiated soil quality among treatments, showing values of moderate quality for the treatments (high, medium, and low doses (0.56, 0.48, 0.40, respectively) and low quality for the control (0.34)). The use of biosolids as an organic amendment improved soil quality by increasing organic matter and microbial growth. Soil quality indices emerges as a practical tool for monitoring the remediation of leachate-contaminated open dump soils in Mexico and similar contexts worldwide.

● Boreal and temperate forests had higher MNC and FNC/BNC than other forest biomes.

Soil microbial necromass carbon (MNC) is an important contributor to soil organic carbon (SOC) and plays a vital role in carbon sequestration and climate change mitigation. However, it remains unclear whether the content, contribution to SOC (MNC/SOC), and fungal-to-bacterial necromass carbon ratio (FNC/BNC) of MNC vary across forest biomes and types. By summarizing data from 1704 points across 93 forest sites, we explored the spatial patterns of MNC, MNC/SOC, and FNC/BNC in the surface layer of 0–20 cm of forest soils, as well as the controlling factors involved. Overall, boreal and temperate forests had higher MNC and FNC/BNC values than tropical, subtropical, and Mediterranean forests, whereas both boreal and Mediterranean forests had low MNC/SOC values. Mixed forests had higher MNC and lower FNC/BNC than broadleaved and coniferous forests, whereas MNC/SOC was higher in broad-leaved forests than that in coniferous forests. Interestingly, the dependence of MNC on forest type also varies among forest biomes. Regression analyses identified soil total N as one of the most important factors affecting MNC and MNC/SOC; whereas MAT, soil pH, and clay content were identified as the important factors affecting FNC/BNC. This synthesis is critical for managing soil MNC to mitigate climate change in forests.

● Loquat orchard location was the main driver of microbial communities and loquat fruit quality.

The role of the soil microbiome in fruit quality within loquat orchards remains largely unknown. In this study, we collected soil samples from various loquat orchards in Ningbo, Zhejiang Province, China and investigated bacterial, fungal, and protist communities. The results showed that soil physicochemical conditions, the microbial community, and loquat fruit quality were significantly related to orchard location but unrelated to cultivation time and fertilization. The heterogeneity of the bacterial community was driven by soil pH, available phosphorus, and available potassium (AK). The fungal community was driven by soil electrical conductivity and AK. The protist community was driven by soil dissolved organic nitrogen and AK. The average fruit weight was significantly correlated with the ɑ- and β-diversity of bacteria and protists as well as the soil multiple nutrient cycling index. Several microbial phyla were related to average fruit weight, while other fruit quality indicators could not be explained by the soil microbiome. Our results reveal that bacterial and protist communities in loquat orchards drive the cycling of multiple nutrients that are related to fruit weight. These insights shed light on the relationship among the soil microbiome, nutrient cycling, and fruit quality, offering valuable scientific guidance for orchard management practices.

● Soils from Poplar, Willow, Black locust plantations were compared to arable soil.

Soil carbon sequestration is regulated by microbial extracellular enzymes. Insight into this process can be gained by studying the relationship between enzyme activity, soil organic carbon and microbial functional genes. The genetic potential of microorganisms to produce carbon cycling enzymes was evaluated in unmanaged plantations of Poplar, Willow, and Black locust, compared with a nearby arable soil. Bacterial and fungal functional genes encoding for cellulase, endoglucanase, endoxylanase and β-glucosidase enzymes were quantified by real-time PCR. The abundance of three out of five genes differed between the treatments. The fungal gene encoding β-glucosidase contributed to the corresponding enzyme activity more than the bacterial one, as evidenced by a positive correlation between gene abundance and enzyme activity (r = 0.42). This gene exhibited a positive correlation with soil organic carbon content (r = 0.42), with higher values in Willow (9 × 10² gene copies µL⁻¹ and 1.4% SOC). These results suggest that the fungal β-glucosidase gene abundance can be regarded as an indicator of increased carbon storage, similarly to the corresponding enzyme activity. The integrated analysis of soil carbon enzyme activities and DNA-based techniques enhanced our comprehension of carbon dynamics by revealing distinct contributions of microbial taxonomic groups to carbon accrual.

● Soil resistomes of conventional and organic systems were similar in terms of ARG biodiversity.

Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes (ARGs) around the globe. In this study, we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices. The organic cropping system was seeded with Triticum spelta without any fertilizer. The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer (NPK), that resulted in an increased amount of total and available carbon and nitrogen in soils. Across all samples, we identified a total of 21 ARG classes, among which the dominant were vancomycin, tetracycline and multidrug. Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil, respectively. Correlation analysis showed significant correlations (positive and negative) among 18 genera and 6 ARGs, as well as between these ARGs and some chemical properties of soils. The analysis of metagenome-assembled genomes revealed that Nitrospirota, Thermoproteota, Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs. Collectively, the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa, including uncultivated genera, in the formation of soil resistome.

● Soil aggregates affect soil respiration and its temperature sensitivity.

Understanding the dynamics of soil respiration, microbial carbon use efficiency (CUE), and temperature sensitivity (Q₁₀) in response to exogenous organic matter (EOM) input, soil aggregate size, and incubation temperature is crucial for predicting soil carbon cycling responses to environmental changes. In this study, these interactions were investigated by 180-day incubation of soil aggregates supplemented with EOM at various temperatures (5°C, 15°C and 25°C). The results reveal an ‘L-shaped’ trend in soil respiration on the time scale across all treatments, characterized by initial rapid declines followed by stability. EOM input and higher temperatures significantly enhance respiration rates. Notably, the respiratory rates of soil aggregates of different sizes exhibit distinct patterns based on the presence or absence of EOM. Under conditions without the addition of EOM, larger aggregates show relatively lower respiration rates. Conversely, in the presence of EOM, larger aggregates exhibit higher respiratory rates. Furthermore, Q₁₀ decreases with increasing aggregate size. The relationship between Q₁₀ and the substrate quality index (SQI) supports the carbon quality temperature (CQT) hypothesis, highlighting SQI’s influence on Q₁₀ values, particularly during later incubation stages. Microbial CUE decreases with EOM input and rising temperatures. Meanwhile, aggregate size plays a role in microbial CUE, with smaller aggregates exhibiting higher CUE due to enhanced nutrient availability. In conclusion, the intricate interplay of EOM input, aggregate size, and temperature significantly shapes soil respiration, microbial CUE, and Q₁₀. These findings underscore the complexity of these interactions and their importance in modeling soil carbon dynamics under changing environmental conditions.

● Pattern and mitigation potential of crop-specific fertilizer-N losses were assessed.

Understanding crop-specific fertilizer-nitrogen (N) loss patterns, driving factors, and mitigation potentials is vital for developing efficient mitigation strategies. However, analyses based on the gross magnitude of fertilizer-N losses within a growing season remain fragmented and inconclusive at a global scale. To address this gap, we conducted a global meta-analysis using 940 observations from 79 published ¹⁵N-tracing studies to assess the effects of natural factors, soil parameters, and N application rates on gross fertilizer-N losses in cereal-cropped soils. We found that China had the highest conventional fertilizer-N application and loss rates (230−255 and 75.9−114 kg N ha⁻¹ season⁻¹, respectively) and the lowest soil organic carbon (SOC) contents (10.6 g kg⁻¹) among the countries examined. Mean annual precipitation, SOC content, and soil pH were key parameters affecting fertilizer-N losses in wheat-, maize-, and rice-cropped soils, respectively. Fertilizer-N application rates were positively correlated with N loss amounts, while higher SOC levels led to lower losses. Adopting optimized N application rates combined with improving SOC levels could potentially mitigate 34.8%−59.6% of N losses without compromising crop yields compared with conventional practices. This study underscores the critical role of SOC in reducing N losses and suggests that future research should focus on innovative strategies and efficient organic amendments for enhanced SOC sequestration.

● Comammox Nitrospira clade A and B showed contrasting responses to citrus planting.

Ammonia oxidizing bacteria (AOB), archaea (AOA), nitrite oxidizing bacteria (NOB) and complete ammonia oxidizers (comammox Nitrospira) are major players in nitrification. However, the distribution and community composition of these nitrifiers in intensively managed orchard soils are still unclear. Here, we chose soil samples from citrus orchards that had been planted for 5 years (5Y), 10 years (10Y), 20 years (20Y) and 30 years (30Y), and adjacent woodland (NF), to study the response of nitrifiers to long-term citrus plantation using quantitative PCR and MiSeq sequencing. Our results revealed that the ammonia and nitrite oxidation potentials in the 5Y soil were the highest, and decreased with increasing plantation age. The AOB abundance was higher in 5Y and 10Y soils than that in 20Y and 30Y soils. The abundance of comammox Nitrospira clade A increased with increasing plantation age, but comammox Nitrospira clade B showed the opposite tendency. MiSeq sequencing results indicated 54d9-like AOA and Nitrobacter-NOB were the dominant populations in 5Y and 10Y soils whereas Nitrososphaera-like AOA and Nitrospira-like NOB dominated in 20Y and 30Y soils. The conversion of woodland to orchard resulted in a significant shift of AOB population from Nitrosospira cluster 3a.1 to cluster 3a.2. In addition, soil pH and phosphorus (P) content were the major factors shaping nitrifying communities. This work suggested citrus plantation altered the distribution of community composition of nitrifiers by affecting soil chemical and physical conditions, and comammox Nitrospira could potentially play an important role in nitrification in intensive managed orchard soils.

● Nutrient constraints in low-fertility soil were modified by different species combinations.

To investigate the interplay of competition and facilitation between plants in low-fertility pasture grasslands of New Zealand, we compared nutrient uptake and acquisition of key nutrients of three species from different functional groups. Combinations of Pilosella officinarum (mouse-eared hawkweed, an invasive weed), Trifolium repens (white clover, a nitrogen fixer) and Dactylis glomerata (cocksfoot, a pasture grass) were planted into a soil with low-to-deficient concentrations of key nutrients. Highest yields were achieved by the grass growing alone but, when the clover and grass had grown together, there were complementary benefits in terms of procurement of a wide range of nutrients from soil despite lower root biomass. The invasive weed negated these benefits, and soil nutrients were exploited less efficiently when Pilosella had grown alone or in a mixture with the other species. Competition from the weed removed the benefits of grass-legume coexistence. These findings are interpreted to suggest that requirements for legumes to be the main source of nitrogen in pasture grasslands may be compromised unless competitive weeds are controlled to avoid disrupted procurement of key nutrients. It is likely these constraints to nutrient procurement would similarly impact conservation grasslands.

● No consistent variation was found in soil respiration Q₁₀ under various O₂ conditions.

Current studies on the temperature sensitivity (Q₁₀) of soil organic matter (SOM) decomposition mainly focus on aerobic conditions. However, variations and determinants of Q₁₀ in oxygen (O₂)-deprived soils remain unclear. Here we incubated three grassland soils under oxic, suboxic, and anoxic conditions subjected to varying temperatures to compare variations in Q₁₀ in relation to changing substrates. No consistent variation was found in Q₁₀ under various O₂ conditions. Further analysis of edaphic properties demonstrated that substrate carbon quality showed a strong influence on Q₁₀ in oxic soils, whereas nitrogen limitation played a more important role in suboxic and anoxic soils. These results suggest that substrate carbon quality and nitrogen limitation may play roles of varying importance in determining the temperature sensitivity of SOM decomposition under various O₂ conditions.

● Afforestation effectively improved soil microbial communities and significantly increased soil nitrogen mineralization rate ( R _m).

Assessing the function of forest ecosystems requires an understanding of the mechanism of soil nitrogen mineralization. However, it remains unclear how soil N-cycling genes drive soil nitrogen mineralization during afforestation. In this study, we collected soil samples from a chrono-sequence of 14, 20, 30, and 45 years of Robinia pseudoacacia L. (RP14, RP20, RP30, and RP45) with a sloped farmland (FL) as a control. Through metagenomic sequencing analysis, we found significant changes in the diversity and composition of soil microbial communities involved in N-cycling along the afforestation time series, with afforestation effectively increasing the diversity (both alpha and beta diversity) of soil microbial communities. We conducted indoor culture experiments and analyzed correlations, which revealed a significant increase in both soil nitrification rate (R_n) and soil nitrogen mineralization rate (R_m) with increasing stand age. Furthermore, we found a strong correlation between soil R_m and soil microbial diversity (both alpha and beta diversity) and with the abundance of soil N-cycling genes. Partial least squares path modeling (PLS-PM) analysis showed that nitrification genes (narH,narY,nxrB, narG,narZ,nxrA, hao, pmoC-amoC) and denitrification genes (norB, nosZ, nirK) had a greater direct effect on soil R_m compared to their effect on soil microbial communities. Our results reveal the relationships between soil nitrogen mineralization rate and soil microbial communities and between the mineralization rate and functional genes involved in N-cycling, in the context of Robinia pseudoacacia L. restoration on the Loess Plateau. This study enriches the understanding of the effects of microorganisms on soil nitrogen mineralization rate during afforestation and provides a new theoretical basis for evaluating soil nitrogen mineralization mechanisms during forest succession.

● Characterization of mollisol soil DOM by untargeted metabolomics is possible.

Mollisol soil is a major contributor to food production. Clarification of the molecular characteristics of dissolved organic matter (DOM) will contribute to the overall understanding and management of mollisol soil. However, the complexity of DOM poses a challenge to understanding its molecular characteristics. In this study, we investigated the molecular characteristics of DOM (< 1000 Da) in mollisol soils with different soil use patterns (forestland and dryland) based on untargeted metabolomics. Here, we confirmed the feasibility of untargeted metabolomics for the molecular characterization of DOM in mollisol soils. DOM in forestland is mainly derived from plant metabolites, and DOM can perform more biological functions. However, DOM in dryland has complex composition and has powerful co-occurrence network interactions due to human activities. Water has better extraction efficiency for polar DOM, while organic reagents can efficiently extract lipid-like DOM, but the polarity of the extractant has less influence on the DOM than the soil physicochemical properties. Meanwhile, 14-dihydroxyzeatin screened based on metabolomics can be used as a potential indicator for corn land. Therefore, untargeted metabolomics can be an effective method to characterize the DOM molecules of mollisol soil, which provides new insights for management of mollisol soil and sustainable agricultural development.

● 6102 high-quality sequencing results of soil bacterial samples were re-analyzed.

Soil organic carbon (SOC) is the largest pool of carbon in terrestrial ecosystems and plays a crucial role in regulating atmospheric CO₂ concentrations. Identifying the essential relationship between soil bacterial communities and SOC concentration is complicated because of many factors, one of which is geography. We systematically re-analyzed 6102 high-quality bacterial samples in China to delineate the bacterial biogeographic distribution of bacterial communities and identify key species associated with SOC concentration at the continental scale. The type of land use was the principal driver of bacterial richness and diversity, and we used machine learning to calculate its influence on microbial composition and their co-occurrence relationship with SOC concentration. Cultivated land was much more complex than forest, grassland, wetland and wasteland, with high SOC concentrations tending to enrich bacteria such as Rubrobacter, Terrimonas and Sphingomona. SOC concentration was positively correlated with the amounts of soil total nitrogen and key bacteria Xanthobacteraceae, Streptomyces and Acidobacteria but was negatively correlated with soil pH, total phosphorus and Micrococcaceae. Our study combined the SOC pool with bacteria and indicated that specific bacteria may be key factors affecting SOC concentration, forcing us to think about microbial communities associated with climate change in a new way.

● Soil pH was a key driver of N₂O emission and sources in acidic soils.

Acidic soil is a main source of global nitrous oxide (N₂O) emissions. However, the mechanism behind the high N₂O emissions from acidic soils remains a knowledge gap. The objective of this microcosm incubation study was to pin-point the microbial mechanisms involved in N₂O production processes in acidic soils. For that purpose, the isotopic signatures and microbial community structure and composition of four soil samples were examined. The results showed that highly acid soils (pH = 3.51) emitted 89 times more N₂O than alkaline soils (pH = 7.95) under the same nitrogen (N) inputs. Fungal denitrification caused high N₂O emissions in acidic soils. ITS to 16S abundance ratio was positively correlated with cumulative N₂O emissions from the tested soils. The highly acid soils (pH < 4.5) showed greater fungal nirK gene abundance and lower abundance of AOA-amoA, AOB-amoA, nirK, nosZ I and nosZ II genes. The unclassified Aspergillaceae fungi (63.65%) dominated the highly acidic soils and was the most strongly correlated genus with N₂O emissions. These findings highlight that soil microbial community structures, denitrifying fungi in particular, shaped by low pH (pH < 4.5) lead to high N₂O emissions from acidic soils.

● Soil erosion decreased soil microbial CUE and increased microbial uptake of carbon.

Soil microbial carbon use efficiency (CUE) is an important synthetic parameter of microbial community metabolism and is commonly used to quantify the partitioning of carbon (C) between microbial growth and respiration. However, it remains unclear how microbial CUE responds to different degrees of soil erosion in mollisol cropland. Therefore, we investigated the responses of soil erosion on microbial CUE, growth and respiration to different soil erosion rates in a mollisol cropland in northeast China based on a substrate independent method (¹⁸O-H₂O labeling). Soils were sampled at four positions along a down-slope transect: summit, shoulder, back and foot. We found microbial CUE decreased significantly with increasing soil erosion rate in 5−20 cm soil, but did not change in 0−5 cm. The decrease of microbial CUE in subsoil was because microbes increased C uptake and allocated higher uptake C to microbial basal respiration with increasing soil erosion rate. Microbial respiration increased significantly with soil erosion rate, probably due to the more disturbance and unbalanced stoichiometry. Furthermore, soil microbes in surface soil were able to maintain their growth rates with increasing degree of erosion. Altogether, our results indicated that soil erosion could decrease microbial CUE by affecting soil physical and chemical properties, resulting in more decomposition of soil organic matter and more soil respiration, which had negative feedbacks to soil C sequestration and climate changes in cropland soil.

● In low-salinity soil, straw-returning did not change necromass contribution to SOC.

Salinization affects microbial-mediated soil organic carbon (SOC) dynamics. However, the mechanisms of SOC accumulation under agricultural management practices in salt-affected soils remain unclear. We investigated the relative contribution of microbial-derived and plant-derived C to SOC accumulation in coastal salt-affected soils under straw-returning, by determining microbial necromass biomarkers (amino sugars) and particulate organic C (POC). Results showed that, straw-returning increased necromass accumulation in low-salinity soil but did not change its contribution to SOC. In medium-salinity soil, straw-returning did not increase necromass accumulation but decreased its contribution to SOC. In low- and medium-salinity soils, the contribution of POC to SOC showed the opposite direction to that of the necromass. These results suggest that under straw-returning, the relative contribution of microbial-derived C to SOC decreased with increasing salinity, whereas the reverse was true for plant-derived C. Our results highlighted that straw-returning reduces the contribution of microbial anabolism to SOC accumulation in salt-affected soils with increasing salinity.

● We studied the effect of nitrogen and biochar on CO₂ emission from SOC and SIC.

Biochar addition generally increases the alkalinity regeneration to resist soil acidification driven by nitrogen (N) fertilization. Calcareous soils contain soil organic carbon (SOC) and inorganic C (SIC). Owing to technical limitations in three-source partitioning CO₂, how biochar addition affects SOC- and SIC-derived CO₂ emission has not been clarified yet. Therefore, we conducted a 70-day incubation experiment of ammonium-N and maize-straw-derived biochar additions to investigate the N plus biochar impacts on SOC- and SIC-derived CO₂ emission. Over the 70-day incubation, we found that the N-only addition increased the SIC-derived CO₂ emission by approximately 41% compared with the control, but decreased the SOC-derived CO₂ emission by approximately 20%. This suggests that the distinct responses of SIC- and SOC-derived CO₂ emission to N-only addition come from N-induced acidification and preferential substrate (N) utilization of soil microorganisms, respectively. Compared with N-only addition, N plus biochar addition decreased the SIC-derived CO₂ emission by 17%−20% during the first 20 days of incubation, but increased it by 54% during the next 50 days. This result suggested that biochar addition reduced the SIC-derived CO₂ emission likely due to the alkalization capacity of biochar exceeding the acidification capacity of ammonium-N in the short term, but it may increase the SIC-derived CO₂ emission induced by the weak acidity produced from biochar mineralization in the long term. This study is helpful to improve the quantification of CO₂ emission from calcareous soils.

● The enzymatic stoichiometry varied between land-use in both soil depth.

This study hypothesized that different land-use affect the microbial enzymatic stoichiometry and C-, N-, and P-acquisition in Brazilian semiarid soils. Thus, the enzymes β-glucosidase (C-acquiring enzyme), urease (N-acquiring enzyme), and acid phosphatase (P-acquiring enzyme) were assessed in soil samples collected at 0−5 and 5−10 cm depth from a tropical dry forest, a protected area with Angico, a protected area with Ipê, scrub area, and an agricultural area with maize. The values of C-, N-, and P-acquiring enzymes were used to calculate the enzymatic C:N, C:P, and N:P ratios. The values of C:P and N:P ratios were higher at 0−5 cm depth, while no significant variation, between soil depth, was observed for C:N ratio. The values of C- and N-acquiring enzymes were higher at 0−5 cm in tropical dry forest areas and Angico forest, respectively. In all land use types, the values of vectors L and A were higher than 1° and 45°, respectively. This study showed that both land-use and soil depth influence the enzymatic stoichiometry, showing higher values of C- and N-acquiring enzymes in native and protected forests at soil surface.

● Some O horizons showed higher nitrification rate than mineral horizons.

High nitrate leaching has been observed from the O horizons of some tropical forests; however, the drivers of high nitrate production (active nitrification) in these O horizons have not yet been identified. This study investigated the drivers of active nitrification in the O horizon of tropical forest soils by focusing on two of the most widely recognized controlling factors of nitrification, total N, and pH. We collected mineral and O horizons from eight tropical forests in Cameroon, Indonesia, and Malaysia and measured gross nitrification rates. Some O horizons showed significantly higher gross nitrification rates than mineral horizons, indicating that these O horizons have a high potential for nitrification. Gross nitrification rates in the O horizons were positively correlated with both total N and pH, and the chemical properties (e.g., total content of N, P, and base cations) were intercorrelated. These correlations suggested that the underlying driver of nitrification in the O horizon was nutrient richness in the litter. Results also indicated a threshold of gross nitrification rates around pH values of 5.5–6.0. We elucidate that active nitrification and subsequent high nitrate leaching from the O horizon could be driven by nutrient-rich litter, possibly derived from soil fertility and tree species.

● The abundance of N-cycling genes differently responded to NPK application.

Straw and manure are widely applied to agricultural systems, and greatly shape soil N-cycling microflora. However, we still lack a comprehensive understanding of how these organic materials structure soil N-cycling microbial communities. In this study, metagenomic analysis was performed to investigate the compositional variation in N-cycling microbial communities in a 30-year long-term experiment under five fertilization regimes: no fertilization (Control), chemical fertilization only (NPK), and NPK with wheat straw (NPK + HS), pig manure (NPK + PM), and cow manure (NPK + CM). Long-term NPK application differentially changed N-cycling gene abundance and greatly altered N-cycling microbial community structure. NPK + HS resulted in a similar pattern to NPK in terms of gene abundance and community structure. However, NPK + PM and NPK + CM significantly increased most genes and resulted in a community similar to that of the Control. Further analysis revealed that serious soil acidification caused by long-term NPK fertilization was a major factor for the variation in N-cycling microbial communities. The addition of alkaline manure, rather than wheat straw, stabilized the N-cycling microbial community structure presumably by alleviating soil acidification. These results revealed the strong impact of soil acidification on microbial N-cycling communities and illustrated the possibility of resolving nitrogen-related environmental problems by manipulating pH in acidified agricultural soils.

● SOC stocks and MCP capacity and efficacy decreased under medium and heavy pollution.

Heavy metal pollution can lead to a great loss of soil organic carbon (SOC). However, the microbial mechanisms that link heavy metal pollution to SOC remain poorly understood. Here, we investigated five apple-orchard soils at different distances from a Pb-Zn smelter. After assessing the heavy metal pollution level based on Grade II of the national soil environmental quality standard (China), we found SOC stocks and microbial carbon pump (MCP) capacity (i.e., microbial residue carbon) under medium and heavy pollution levels were significantly lower than those under safe, cordon and light pollution levels. The structural equation model showed causality in the SOC variations linked to pollution level through MCP capacity, which could contribute 77.8% of the variance in SOC storage. This verified MCP capacity can serve as a key parameter for evaluation of SOC storage under heavy metal pollution. Soil MCP efficacy, i.e., the proportion of microbial residue carbon to SOC, also decreased under medium and heavy pollution. This suggested that, with a heavier pollution level, there was a higher rate of reduction of microbial residue carbon in soil than the rate of reduction of SOC. As MCP efficacy can be a useful assessment of SOC stability, the significantly positive relationship between MCP efficacy and clay content in correlation analysis implied that lower MCP efficacy was correlated with SOC stability under the heavier pollution level. Our study provides valuable insights to identify the mechanisms of microbially mediated C transformation processes that are influenced by heavy metal pollution in agroecosystems.

● The bacterial and fungal diversity decreased greater in 5%−36% DRW than 5%−25% DRW.

Altered drying-rewetting (DRW) procedures due to climate change may influence soil microbial properties and microbially-mediated carbon cycling in arid and semi-arid regions. However, the effects of DRW of different intensities on the microbial properties and respiration are not well understood. Thus, the responsive patterns of microbial communities and carbon mineralization in agriculture soil on the Chinese Loess Plateau to DRW treatments with different wetting intensities (5%−25% and 5%−36%) and frequency (1-cycle to 4-cycle) were investigated. Continuous moisture levels of 5%, 25% and 36% were used as control. Results revealed that the reduction of bacterial diversity and richness were greater for 5%−36% than 5%−25% treatment, while diversity of fungi was similar for different wetting intensities. Bacterial communities became clustered by wetting intensity rather than cycle number, however fungal community was unaffected by DRW. The complexity of bacterial co-occurrence network increased because of higher nodes, edges, average degree, diameter and average cluster coefficient after 4-cycles, and the interaction was more complex after 1-cycle for fungi. Rewetting caused a pulse-like increase of respiration rate, and the pulse amplitude was greater for DRW with high rewetting intensity and decreased with the increase of cycle number. The cumulative CO₂ emission for DRW treatments was lower than that for the continuous moisture conditions. The net reduction of carbon release for 5%−36% treatment was 1.18 times higher than that for 5%−25% treatment. Our study provides experimental evidence of the positive potential of DRW processes for maintaining soil carbon stock in an agriculture system on the Loess Plateau.

● On average conventional tillage outperformed no tillage.

Reduced tillage practices present a tool that could sustainably intensify agriculture. The existing literature, however, lacks a consensus on how and when reduced tillage practices should get implemented. We reanalyzed here an extensive dataset comparing how regular tillage practices (i.e., conventional tillage) impacted yield of eight crops compared to stopping tillage altogether (i.e., no-tillage practice). We observed that aridity and fertilization favored no tillage over conventional tillage whereas conventional tillage performed better under high fertility settings. We further show that the responses are consistent across the crops. Our reanalysis complements the original and fills a gap in the literature questioning the conditions under which reducing tillage presents a viable alternative to common tillage practices.

● This study reviewed the contribution of carbonates to soil CO₂ emissions.

In calcareous soils, recent studies have shown that soil-derived CO₂ originates from both soil organic carbon (SOC) decomposition and soil inorganic carbon (SIC) dissolution, a fact often ignored in earlier studies. This may lead to overestimation of the CO₂ emissions from SOC decomposition. In calcareous soils, there is a chemical balance between precipitation and dissolution of CaCO₃-CO₂- {\text{HCO}}_{\text{3}}^{\text{–}}, which is affected by soil environmental factors (moisture, temperature, pH and depth), root growth (rhizosphere effect) and agricultural measures (organic materials input, nitrogen fertilization and straw removal). In this paper, we first introduced the contribution of SIC dissolution to CO₂ emissions from calcareous soils and their driving factors. Second, we reviewed the methods to distinguish two CO₂ sources released from calcareous soils and quantify the ¹³C fractionation coefficient between SIC and SIC-derived CO₂ and between SOC and SOC-derived CO₂, and to partition three CO₂ sources released from soils with plants and organic materials input. Finally, we proposed methods for accurately distinguishing three CO₂ sources released from calcareous soils. This review helps to improve the accuracy of soil C balance assessment in calcareous soils, and also proposes the direction of further investigations on SIC-derived CO₂ emissions responses to abiotic factors and agricultural measures.

● Soil acidification caused severe losses of soil inorganic carbon stock worldwide.

Soil inorganic carbon (SIC) accounts for about half of the C reserves worldwide and is considered more stable than soil organic carbon (SOC). However, soil acidification, driven mainly by nitrogen (N) fertilization can accelerate SIC losses, possibly leading to complete loss under continuous and intensive N fertilization. Carbonate-free soils are less fertile, productive, and more prone to erosion. Therefore, minimizing carbonate losses is essential for soil health and climate change mitigation. Rock/mineral residues or powder have been suggested as a cheaper source of amendments to increase soil alkalinity. However, slow mineral dissolution limits its efficient utilization. Soil microorganisms play a vital role in the weathering of rocks and their inoculation with mineral residues can enhance dissolution rates. Biochar is an alternative material for soil amendments, in particular, bone biochar (BBC) contains higher Ca and Mg that can induce even higher alkalinity. This review covers i) the contribution and mechanism of rock residues in alkalinity generation, ii) the role of biochar or BBC to soil alkalinity, and iii) the role of microbial inoculation for accelerating alkalinity generation through enhanced mineral dissolution. We conclude that using rock residues/BBC combined with microbial agents could mitigate soil acidification and SIC losses and also improve agricultural circularity.

● This study reviewed the effect of warming on microbial carbon use efficiency (CUE).

Microbial carbon use efficiency (CUE) is an important factor driving soil carbon (C) dynamics. However, microbial CUE could positively, negatively, or neutrally respond to increased temperature, which limits our prediction of soil C storage under future climate warming. Experimental warming affects plant production and microbial communities, which thus can have a significant impact on biogeochemical cycles of terrestrial ecosystems. Here, we reviewed the present research status of methods measuring microbial CUE and the response of microbial CUE to the changes of biotic and abiotic factors induced by warming. Overall, current measurement methods mainly include metabolic flux analysis, calorespirometry, stoichiometric model, ¹³C and ¹⁸O labeling. Differences in added substrate types can lead to an overestimation or underestimation on microbial CUE, particularly when using the ¹³C labeling method. In addition, changes in the dominant microbial community under warming may also affect CUE. However, there is still uncertainty in CUE characteristics of different microorganisms. Microbial CUE is generally decreased under warming conditions as microbes are subjected to water stress or soil labile organic matter is much more depleted compared to ambient conditions. In contrast, considering that warming increases soil nutrient availability, warming may enhance microbial CUE by alleviating nutrient limitations for microbes. In conclusion, the response of microbial CUE to warming is more complex than expected. The microbial growth and physiological adaptation to environmental stress under warming is one of the main reasons for the inconsistence in microbial CUE response. Finally, we propose five aspects where further research could improve the understanding of microbial CUE in a warmer world, including using new technologies, establishing multi-factor interactive experiments, building a network of experimental research platform for warming, and strengthening studies on response of CUE to warming at different soil depths and on different temporal scales.