● 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.

● Land use type affects the physicochemical properties of soil.

Soil fertility is affected by land-use types and land management, which exacerbates soil erosion and various other forms of soil degradation in the mountainous regions of Vietnam. This study was conducted in A Luoi District, Thua Thien Hue, Vietnam to identify the effects of land-use types on specific soil physicochemical characteristics related to soil fertility. Soil physicochemical properties, such as organic matter (OM), total nitrogen (TN), total phosphorous (TP), and K⁺ were significantly affected by land-use type. The results showed that the soils were sandy in rice but clay loam for acacia and cassava. The mean bulk density value of acacia soil was significantly greater than that of other soils. TN were higher in the acacia soils than those in the rice, maize, and banana soils. The OM content was significantly higher in the acacia, cassava, and banana soils than those in the rice and maize soils. The mean of exchangeable K⁺ in the rice soil was higher compared to those in other soils and was affected by land-use type. The high exchangeable acidity content in the soils was probably due to intensive precipitation. However, both land use type and management did not affect the CEC value. Overall, the inappropriate land use caused the disturbance of soil physicochemical properties, indicating that the conditions of rice and maize soils are becoming worse than acacia soils. Therefore, lowering the intensity of cultivation, adopting incorporated soil fertility management, and applying organic fertilizer should preserve the existing conditions and enhance soil properties.

● LDPE had no effect on the mortality, growth, and reproduction of earthworms.

Cadmium (Cd) can accumulate in the food chain, with serious impacts on human health and safety. Microplastics (MPs) such as low-density polyethylene (LDPE) should be considered not only as a single pollutant but also as a carrier of other pollutants. In this study, we investigated the joint effects of 30% LDPE and 313 mg kg⁻¹ Cd on mortality, growth, reproduction, microstructure, DNA damage, oxidative stress, and mRNA levels in the earthworm Eisenia fetida. We found that 313 mg kg⁻¹ Cd inhibited growth and reproduction and damaged the microstructures of the skin and intestine. Meanwhile, LDPE had no effect on the mortality, growth, or cocoon production of earthworms. Moreover, it did not increase the mortality, growth, or inhibition of cocoon production caused by Cd and instead alleviated the DNA damage in coelomocytes caused by Cd treatment. Finally, it did not alter the accumulation of Cd in the worms. These indicators can be used for toxicity safety assessment and soil ecological risk assessment of LDPE and Cd cooccurrence in soil.

● N fertilizer altered bacterial community compositions by changing soil nutrients.

Nitrogen (N) fertilization drives the structure and function of soil microbial communities, which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability. Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated, it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members. Here, we examined the effects of five N fertilization levels (0, 135, 180, 225, and 360 kg N ha⁻¹) on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils. The results showed that N addition altered microbial community composition, which were positively related to soil total N and available phosphorus (P) contents. The abundance of ammonia-oxidizing archaea (AOA) significantly decreased after N addition, whereas ammonia-oxidizing bacteria (AOB) increased in N360 treatment. Compared with low-N group (N0 and N135), the high-N group (N225 and N360) shaped more complex microbial webs and thus improved the stability of the microbial community. Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group (0.83) than the low-N group (0.49). Although there were more positive links across all microbial networks, the proportion of negative links significantly increased in the high-N network, suggesting that excess N addition aggravated the competition among microbial species. Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production. Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.

● 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.

● Flue gas desulfurization gypsum and clover planting alleviated the soil salinization stress.

The coastal area of Shandong Province, characterized by coastal saline tidal soil, is one of the main production areas of winter jujube in China. However, the low soil fertility and poor soil structure in jujube orchard restricted the development of the jujube industry. The objectives of this study were to 1) evaluate the effect of application of flue gas desulfurization (FGD) gypsum and clover planting on soil quality improvement and soil microbial community structure of jujube orchard; 2) investigate the effects of two measures on the nutrition and quality of winter jujube. The results showed that FGD gypsum reduced the soil total salt content by 65.6%, and clover planting increased the soil organic matter content by 30.7%, which effectively alleviated the soil salinization stress and improved the soil structure. Soil pH and total phosphorus (TP) were the main determinants influencing bacterial community composition, and TP was the dominant factor of the fungal community composition in the saline-alkali soils. Meanwhile, FGD gypsum addition and clover planting significantly increased the sugar degree and Vc content of winter jujube, thus improved jujube quality, and further contributed to the ecological sustainable development of winter jujube industry.

● Metatranscriptomics uncovers the dynamic expression of functional genes in soil environments, providing insights into the intricate metabolic activities within microbial communities.

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by, and functional activities of, the microbial community across diverse ecosystems at a given time, thereby shedding light on their metabolic responses to the prevailing environmental conditions. The double-RNA approach involves the simultaneous analysis of rRNA and mRNA, also termed structural and functional metatranscriptomics. By contrast, mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles, but requires either deep sequencing or effective rRNA depletion. In this review, we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics. In particular, we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields, such as rhizobiomes, antibiotic resistomes, methanomes, and viromes. Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

● Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages.

Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.

● Response of growth rate and antioxidative system of ten Bacillus strains to acid stresses was assayed.

Environmental changes including soil acidification exert obvious stresses on soil ecosystems and influence soil microorganisms. In this study, ten microbial strains were incubated under different acid treatments to investigate responses of microbial growth and antioxidative system to acid stress. All the strains belong to Bacillus genus, but exhibit distinct ecological functions. We observed that these microbial strains had obviously different pH tolerance threshold, in spite of the close phylogenetic classification among strains. Acid stresses exerted significant effects on microbial antioxidative system, including superoxide dismutase (SOD), catalase (CAT) and glutathione transferring enzymes (GPX and GR) and reactants (GSH and GSSH), but the effects were strain specific. Furthermore, we found acid stress effects on total variances of the investigated microbial antioxidative system along the first two principal components (PCs). Activities of CAT and SOD contributed substantially to PC1 that reflected obvious acid effects on NC7 and ZC4, and closely related to intracellular malondialdehyde content. The GSSG activities and GSH/GSSG contributed greatly to PC2 that unveiled acid stress effects on most of the microbial strains. Our results highlight substantially heterogeneous responses of microbial strains to acid stress and support that phylogenetic closeness does not imply functional similarity of soil microorganisms under environmental changes.

● Salt spray is a natural disturbance in coastal area of Southern China.

Salt spray is a natural disturbance in coastal region. Arbuscular mycorrhizal fungi (AMF) are recognized as bio-ameliorators of soil salinity in plants. However, the mechanism through which AMF protects Cinnamomum camphora against aerial salinity remains unclear. To address this knowledge gap, plants were subjected to four fungal regimes, namely sterilized fungal inoculum, Glomus tortuosum, Funneliformis mosseae, or a combination of these two fungi, and exposed to three sprayed-salt regimes (0, 7, or 14 mg NaCl cm⁻² d⁻¹) in a greenhouse. Salt spray significantly decreased photosynthetic capabilities, total dry weight, and salinity tolerance of non-mycorrhizal plants. Mycorrhizal inoculation, particularly a combination of G. tortuosum and F. mosseae, evidently mitigated the detrimental effects induced by salt spray. Meanwhile, mycorrhiza-mediated protection depended on the intensity of sprayed salt and the identity of fungal taxa. Furthermore, the enhanced resistance of mycorrhizal C. camphora seedlings to aerial salinity was mainly owing to increased leaf thickness and photosynthetic capabilities. These findings imply that inoculation with combined fungi could be an optimal strategy for cultivating C. camphora plants in coastal regions. The results gained hold the potential to offer both theoretical and practical guidance for the managers of coastal ecosystems in soil restoration and conservation.

● A new COX1 primer for soil nematode metabarcoding was designed, and this primer outperforms other commonly used COX1 primer pairs in species recovery and quantity of PCR products.

Microscopic nematodes play important roles in soil ecosystems and often serve as bioindicators of soil health. The identification of soil nematodes is often difficult due to their limited diagnostic characters and high phenotypic plasticity. DNA barcoding and metabarcoding techniques are promising but lack universal primers, especially for mitochondrial COX1 gene. In this study a degenerated COX1 forward primer COIFGED was developed. The primer pair (COIFGED/JB5GED) outperforms other four commonly used COX1 primer pairs in species recovery and quantity of polymerase chain reaction (PCR) products. In metabarcoding analysis, the reads obtained from the new primer pair had the highest sequencing saturation threshold and amplicon sequence variant (ASV) diversity in comparison to other COX1 as well as 18S rRNA primers. The annotation of ASVs suggested the new primer pair initially recovered 9 and 6 out of 25 genera from mock communities, respectively, outperformed other COX1 primers, but underperformed the widely used 18S NF1/18Sr2b primers (16 out of 25 genera). By supplementing the COX1 database with our reference sequences, we recovered an additional 6 mock community species bringing the tally closer to that obtained with 18S primers. In summary, our newly designed COX1 primers significantly improved species recovery and thus can be supplementary or alternative to the conventional 18S metabarcoding.

● Integrated grain cropping systems promote soil health (SH) and sustainability.

Tropical soils are prone to degradation. Adoption of conservation agricultural practices is essential to improve soil health, which is influenced by soil microbes. In this study we analyzed shifts in microbial biomass and activity (MBA) and microbial community structure (MCS) based on fatty acid methyl esthers (FAMEs) between five no-till agricultural practices: maize monoculture (MM); maize annualy intercropped with Urochloa decumbens (M/Ud); M/Ud with soybean rotation every other year (M/Ud–S); M/Ud keeping the pasture for the next two years (M/Ud–Ud–Ud); and maize intercropped with U. ruziziensis keeping the pasture for the next two years (M/Ur–Ur–Ur). Results indicated that MBA was affected by the inclusion of Urochloa intercropping and by rotation with soybean. Systems under a longer residence time with Urochloa in the field had higher β-glucosidase activity and soil basal respiration, indicating a greater microbial activity. MCS was less affected than MBA by the investigated cropping systems. MCS changed only in the continuous pasture systems, which were enriched in arbuscular mycorrhyzal fungi (AMF). Additionally, the continuous pasture systems had lower microbial stress ratios than the other agricultural practices. In sum, our study showed that utilization of Urochloa spp. under longer periods in no-till agricultural practices contributes to increase microbial activity, AMF abundance and decrease microbial stress ratio. These changes are primarily beneficial for soil health.

● The nitrogen (N) and phosphorus (P) addition promotes the abundance of soybean soil nematodes.

With global warming, the increasing of industrial and agricultural activities and demand for fossil fuels, large amounts of nitrogen and phosphorus compounds are released into the atmosphere, resulting in an annual increase in nitrogen and phosphorus deposition. The nematodes, as one of the main functional groups of soil organisms, occupy multiple trophic levels in soil detritus food networks. However, few studies on the effects of nitrogen and phosphorus on soil nematodes, and the results are uncertain. This experiment was conducted in soybean farmland and four treatments included control, nitrogen addition, phosphorus addition, and N + P addition. The results showed that both phosphorus and N + P addition significantly increased the abundance of soil nematodes, but that had no effects on soil nematodes richness. Redundancy analysis showed that nitrate nitrogen, soil moisture content, and pH were environmental factors driving different dietary changes in soil nematode communities. The effect of phosphorus addition on the abundance of nematode communities mainly affects ammonium nitrogen. Our findings revealed that nitrogen addition when phosphate fertilizer is added to soybean farmland will have a certain positive effect on the soil underground food web, which provides a basis for better explaining the effect of nitrogen and phosphorus addition on soybean farmland.

● Herbicide-based weeds control impacts wheat crops as well.

To address environmental concerns and manage resistant weeds, there is a growing demand for eco-friendly alternatives. In this study, we propose the integration of synthetic communities (SynComs) to reduce herbicide consumption. Four SynComs, consisting of bacteria isolated from weed or wheat rhizospheres, were first evaluated under greenhouse conditions. All SynComs enhanced wheat growth, which was manifested by increased Soil Plant Analysis Development (SPAD) values and fresh biomass. At the same time, SynCom C4 effectively reduced SPAD values and fresh biomass of the infesting weed, Phalaris minor, when combined with low-dose Axial herbicide. A field trial was then conducted using the C4 SynCom and various doses of Axial (100%, 75%, 50%, and 25%). Remarkably, the combination of C4 with 50% and 75% Axial significantly improved wheat growth by mitigating the side effects of herbicide on wheat. Weed infestation reduced grain yield by 16% and 25% at the dose of 50% and 75% Axial, respectively. The combination of Axial with C4 rescued up to 22% of grain yield loss under infested weed compared with Axial alone. Our findings suggested that the combination of herbicides with SynComs exhibited synergistic effects for controlling Phalaris minor and promoting wheat growth, so that such combination provides a sustainable and eco-friendly weed control strategy.

● Nematode identification serves as an important parameter to study their behaviour, importance and pathogenicity.

Nematodes constitute most diverse and least studied group of soil inhabiting invertebrates. They are ecologically and physiologically important, however, wide range of nematodes show harmful impact on the individuals that live within their vicinity. Plant parasitic nematodes (PPNs) are transparent, pseudocoelomate, free living or parasitic microorganisms. PPNs lack morphometric identification methods due to insufficient knowledge on morphological variations among closely related taxa. As such, molecular approaches such as DNA and protein-based information, microarray, probing, sequence-based methods and others have been used to supplement morphology-based methods for their identification. To invade the defense response of different plant species, parasitic nematodes have evolved different molecular strategies. Ascarosides and certain protein-based nematode-associated molecular patterns (NAMPs), can be perceived by the host plants, and can initiate a signaling cascade. To overcome the host confrontation and develop certain nematode feeding sites, some members can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling. This review primarily emphasizes on an updated account of different classical and modern tools used for the identification of PPNs. Besides we also summarize the mechanism of some important signaling pathways which are involved in the different plant nematode interactions.

● Microbial attributes were compared between soil fauna gut and plant rhizosphere.

Diverse microbes inhabit animals and plants, helping their hosts perform multiple functions in agricultural ecosystems. However, the responses of soil fauna gut and plant rhizosphere microbiomes to livestock manure applications are still not well understood. Here we fed Protaetia brevitarsis larvae (PBL) with chicken manure and collected their frass. The frass and manure were applied as fertilizers to lettuce pots. We then compared the changes of microbial diversity, community assembly, and potential functions between the gut group (i.e., all PBL gut and frass samples) and the rhizosphere group (i.e., all rhizosphere soil samples). We revealed that manure applications (i.e., feeding or fertilization) decreased bacterial diversity in the gut group but increased that in the rhizosphere group. Particularly, the proportions of Bacilli in the gut group and Gammaproteobacteria in the rhizosphere group were increased (up to a maximum of 33.8% and 20.4%, respectively) after manure applications. Stochastic and deterministic processes dominated community assembly in the gut and rhizosphere microbiomes, respectively. Manure applications increased the microbial co-occurrence network complexity of both the gut and rhizosphere groups. Moreover, the proportions of functional taxa associated with human/animal pathogens in the gut group and carbon/nitrogen cycling in the rhizosphere group were enhanced (up to 2.6-fold and 24.6-fold, respectively). Our findings illustrate the different responses of microbial diversity, community assembly, and potential functions in soil fauna gut and plant rhizosphere to manure applications. The results could enhance our knowledge on the reasonable utilization of animal and plant microbiomes in agricultural management.

● The use of human excrement as fertilizer is a characteristic of traditional Chinese agriculture.

The use of human excrement in fertilization is a major attribute differentiating the Chinese traditional agriculture from the agriculture in other regions around the world. Despite the fact that the exact record showing that human excrement was used as fertilizer in China emerged in the Western Han Dynasty (B.C. 202–A.D. 8), such records did not become prevalent until the Southern Song Dynasty (A.D.1127−1279). In the Ming and Qing eras (A.D.1368−1912), human excrement was even considered “top-class fertilizer” and served as the most essential fertilizer in farmland fertilization. The importance of human excrement in the Ming and Qing was mainly reflected by farmers’ purchase of human excrement from urban areas. As fertilization practices became increasingly popular during the period, men of letters built a localized theoretical system centering on human excrement. Although the use of human excrement had both positive and negative impacts on public health and the ecological environment, the positive overshadowed the negative as a whole. Today, it is worth pondering on how the utilization of human excrement as an agricultural resource can be improved so that a material cycle system can be rebuilt to re-connect the urban and rural areas.

● ARB was investigated in different soil types following manure application.

Swine manure, commonly applied as organic compost in agricultural fields, is an important reservoir of antibiotic-resistant bacteria (ARB). Previous work indicated that manure application led to more antibiotic resistance genes in red soil compared with black soil and fluvo-aquic soil. Accordingly, the influencing mechanisms of soil types on the distribution of ARB was worthy of further exploration by a soil column experiment. The results showed that a higher shift in the operational taxonomic units and the community composition of chlortetracycline (CTC)-resistant bacteria (CRB) were observed in fluvo-aquic soil than in black and red soils. CTC induced antibiotic resistance development in soil indigenous microorganisms (Streptomyces, Pseudomonas, Bacillus, Rhodococcus, and Paenibacillus), and the induction was most obvious in fluvo-aquic soil. Streptomyces was significantly positively correlated with pH and organic matter. Additionally, LEfSe analysis indicated that the key different genera were Microbacteriaceae (black soil), Lactobacillus, unclassified_c__Bacilli and Paenibacillus (fluvo-aquic soil), and Dyella, Ralstonia and Bacillus (red soil). It was concluded that manure application led to higher CRB risk in fluvo-aquic soil compared with black and red soils. Overall, appropriate methods according to soil types are important ways to reduce the risk of soil resistant bacteria during manure return.

● The unique gut habitat led to a core intestinal microbiome in diverse soil ecosystems.

Soil invertebrates are widely distributed in the ecosystem and are essential for soil ecological processes. Invertebrate gut microbiome plays an important role in host health and has been considered as a hidden microbial repository. However, little is known about how gut microbiome in soil invertebrates respond to diverse soil ecosystems. Based on a laboratory microcosm experiment, we characterized the assembling of microbiome of soil collembolans (Folsomia candida) from six representative regions of the soil ecosystem which they inhabit. Results showed that collembolan gut microbial communities differed significantly from their surrounding soil microbial communities. A dominant core gut microbiome was identified in gut habitat. Community analyses indicated that deterministic process dominated in the community assembly of collembolan gut microbiome. The results further demonstrate a dominant contribution of host selection in shaping gut microbiome. It is also worthy to mention that pathogens, such as common agricultural phytopathogenic fungi Fusarium, were involved in core microbiome, indicating that collembolans could act as vectors of pathogens. Our results unravelled the existence of gut core microbiome of collembolans in soil ecosystems and provided new insights for understanding the crucial role of gut microbiome of soil fauna in maintaining microbial biodiversity and stability of soil ecosystems.

● CH₄ emission rates followed an increased pattern during the growing season at Tibetan Plateau.

Microorganisms play pivotal roles in soil methane (CH₄) emissions and their functional genes are origins of a key mechanism for soil CH₄-cycling. However, understanding of the roles of specific genes (e.g., unique or shared genes carried by species) underlying CH₄-cycling remains elusive. Here, we measured CH₄ emission rates and investigated variations in microbial community and the abundance of genes carried by species during the growing season in alpine meadow on the Tibetan Plateau. We discovered that CH₄ emission rates increased from 394.4, 745.9, and 1092.7 µg CH₄ m⁻² h⁻¹, in April, June, and August, respectively, and had a positive correlation with unique genes carried by abundant species during the growing season. Moreover, we found that unique genes carried by abundant species involved in methanogenesis processes have a higher abundance than methanotrophic processes. Further analysis indicated that climate factors (i.e., mean monthly temperature (MMT) and mean monthly precipitation (MMP)) influenced microbial community and their functional genes, and therefore affected the CH₄ emission rates. Overall, the present study provides a novel insight into the variation of soil CH₄ emissions from a functional gene perspective, highlighting the important roles of unique genes carried by abundant species in CH₄ emissions in the Tibetan Plateau under seasonal variation.