Long-term warming increased carbon sequestration capacity in a humid subtropical forest.

Tropical and subtropical forests play a crucial role in global carbon (C) pools, and their responses to warming can significantly impact C-climate feedback and predictions of future global warming. Despite earth system models projecting reductions in land C storage with warming, the magnitude of this response varies greatly between models, particularly in tropical and subtropical regions. Here, we conducted a field ecosystem-level warming experiment in a subtropical forest in southern China, by translocating mesocosms (ecosystem composed of soils and plants) across 600 m elevation gradients with temperature gradients of 2.1°C (moderate warming), to explore the response of ecosystem C dynamics of the subtropical forest to continuous 6-year warming. Compared with the control, the ecosystem C stock decreased by 3.8% under the first year of 2.1°C warming; but increased by 13.4% by the sixth year of 2.1°C warming. The increased ecosystem C stock by the sixth year of warming was mainly attributed to a combination of sustained increased plant C stock due to the maintenance of a high plant growth rate and unchanged soil C stock. The unchanged soil C stock was driven by compensating and offsetting thermal adaptation of soil microorganisms (unresponsive soil respiration and enzyme activity, and more stable microbial community), increased plant C input, and inhibitory C loss (decreased C leaching and inhibited temperature sensitivity of soil respiration) from soil drying. These results suggest that the humid subtropical forest C pool would not necessarily diminish consistently under future long-term warming. We highlight that differential and asynchronous responses of plant and soil C processes over relatively long-term periods should be considered when predicting the effects of climate warming on ecosystem C dynamics of subtropical forests.

Elevated CO2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure.

Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.

Long-term seawall barriers lead to the formation of an urban coastal lagoon with increased antibiotic resistome.

Urbanization has increased the spread of antibiotic resistance genes (ARGs) impacting urban aquatic ecosystems and threatening human health. However, an overview of the antibiotic resistome in artificial coastal lagoons formed by coastal seawall construction is unclear. This study investigated the resistome of sediment in a coastal lagoon, established for over 60 years and found that the composition of the resistome in the lagoon sediments associated with the seawall significantly differed from that of marine sediment external to the seawall. Moreover, the diversity, number, relative abundance, and absolute abundance of the antibiotic resistome in the lagoon sediments were significantly higher compared to marine sediment. Network analyses revealed that more co-occurrences were found in lagoon sediment between bacterial communities, ARGs and mobile genetic elements (MGEs) than in marine sediments, suggesting that bacteria in lagoon sediments may be associated with multiple antibiotic resistances. Random forest and structural equation models showed that an increase in the absolute abundance of MGEs had a concomitant effect on the absolute abundance and diversity of ARGs, whereas increasing salinity decreased the absolute abundance of ARGs. This study provides a basis to assess the risk of resistome diffusion and persistence in an artificial coastal lagoon.

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming.

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.

Acidity of Soil and Water Decreases in Acid-Sensitive Forests of Tropical China.

Acid deposition in China has been declining since the 2000s. While this may help mitigate acidification in forest soils and water, little is known about the recovery of soils and water from previous severe acidification in tropical China. Here, we assessed the chemistry of mineral soils, water, and acid gases (SO2 and NOx) from three successional forest types in tropical China from 2000 to 2022. Our results showed that soil pH increased synchronously from 3.9 (2000-2015) to 4.2 (2016-2022) across all three forest types, with exchangeable acid initially decreasing and thereafter stabilizing. Surface and ground water pH also gradually increased throughout the monitoring period. Soil pH recovery was stronger in the primary than in the planted forest. However, soil pH recovery lagged behind the increase in rainfall pH by approximately a decade. The recovery of soil pH was likely related to the positive effects of the dissolution of Al/Fe-hydroxysulfate mineral and subsequent sulfur desorption on soil acid-neutralizing capacity, increased soil organic matter, and climate warming, but was likely moderated by increased exchangeable aluminum and potentially proton-producing hydroxysulfate mineral dissolution that caused the lagged soil pH recovery. Surface and ground water pH recovery was attributed to increased water acid-neutralizing capacity. Our study reports the potential for the recovery of acidified soil and water following decreased acid deposition and provides new insights into the functional recovery of acid-sensitive forests.

Antibiotic resistome in groundwater and its association with mountain springs and river.

The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial ß-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.

Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere.

The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.

Impacts of global change on the phyllosphere microbiome.

Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.

HiLi-chip: A high-throughput library construction chip for comprehensive profiling of environmental microbial communities.

Investigating the contribution and associations of environmental microbes to ecological health and human well-being is in great demand with the goal of One Health proposed. To achieve the goal, there is an urgent need for accurate approaches to obtaining a large amount of high-resolution molecular information from various microbes. In this study, we developed a high-throughput library construction chip (HiLi-Chip) for profiling environmental microbial communities and evaluated its performance. The HiLi-Chip showed high conformity with the conventional Pacbio method in terms of α-diversity, community composition of abundant bacteria (>83%), as well as rare taxa (>84%) and human pathogens detection (>67%), indicating its advantages of accuracy, high-throughput, cost-efficiency, and broad practicability. It is suggested that the optimal strategy of the HiLi-Chip was a 2.4 µL PCR mixture per sample (∼2.4 ng DNA) with a 216-sample × 24-replicate format. We have successfully applied the HiLi-Chip to the Jiulongjiang River and identified 51 potential human bacterial pathogens with a total relative abundance of 0.22%. Additionally, under limited nutrients and similar upstream environments, bacteria tended to impose competitive pressures, resulting in a more connected network at the downstream river confluence (RC). Whereas narrow niche breadth of bacteria and upstream environmental heterogeneity probably promoted niche complementary and environment selection leading to fewer links at RC in the midsection of the river. Core bacteria might represent the entire bacterial community and enhance network stability through synergistic interactions with other core bacteria. Collectively, our results demonstrate that the HiLi-Chip is a robust tool for rapid comprehensive profiling of microbial communities in environmental samples and has significant implications for a profound understanding of environmental microbial interactions.

[High-throughput qPCR and Amplicon Sequencing as Complementary Methods for Profiling Antibiotic Resistance Genes in Urban Wetland Parks].

Urban wetland parks are an important practice for urban wetland protection and utilization due to the vast ecosystem service value. As emerging contaminants, antibiotic resistance genes (ARGs) are great attractions for environmental research and public concerns. Based on high-throughput qPCR and high-throughput amplicon sequencing techniques, we investigated the occurrence, abundance, and distribution profiles of antibiotic resistance genes in the aquatic environment of Xiamen urban wetland parks (five sites). The influencing factors and driving mechanisms of antibiotic resistance genes were deciphered on the basis of microbial community structure and water quality. Diverse and abundant ARGs were observed and coexisted in urban wet parks. A total of 217 ARGs were detected in the water body of urban wetland parks, with an abundance up to 6.48×109 copies·L-1. Urban wetland parks were important hotspots and repositories of the antibiotic resistome. A total of nine bacterial genera, including Marivivens, NS5_marine_group, and Planktomarina, were identified as the potential carriers of diverse resistance genes (41 ARGs). The microbial communities could alone explain 51% of alterations in the antibiotic resistome in the aquatic environment of the urban wetland parks. Therefore, the microbial community was the key driving force for the occurrence and evolution of ARGs in urban wetland parks. Based on the results, with the presence of ARGs and antibiotic resistance bacteria, it is suggested that the water environments of urban wetland parks have potential risks of water ecological security and human health, and it is necessary to further enhance the research and control of microbial contaminants in the aquatic environment of urban wetland parks.

Mapping the profiles and underlying driving mechanisms of the antibiotic resistome and microbiome within a subtropical complex river watershed.

Antibiotic resistance is an escalating global concern, leading to millions of annual deaths worldwide. Human activities can impact antibiotic resistance gene (ARG) prevalence in aquatic ecosystems, but the intricate interplay between anthropogenic disturbances and river system resilience, and their respective contributions to the dynamics of different river segments, remains poorly understood. In this study, we investigate the antibiotic resistome and microbiome in water and sediment samples from two distinct sub-watersheds within a specific watershed. Results show a decrease in the number of core ARGs downstream in water, while sediments near densely populated areas exhibit an increase. PCoA ordination reveals clear geographic clustering of resistome and microbiome among samples from strong anthropogenic disturbed areas, reservoir areas, and estuary area. Co-occurrence networks highlight a higher connectivity of mobile genetic elements (MGEs) in disturbed areas compared to reservoir areas, presenting a threat to densely populated areas. Water quality parameters and antibiotics concentration were the key factors shaping the ARG profiles in sediment samples from urban regions. Overall, our study reveals distinct patterns of ARGs in sediment and water samples, emphasizing the importance of considering both anthropogenic and natural factors in comprehending and managing ARG distribution in river systems.

Mixed plantations do not necessarily provide higher ecosystem multifunctionality than monoculture plantations.

Forest stand transformation is a crucial strategy for enhancing the productivity and stability of planted forest ecosystems and maximizing their ecosystem functions. However, understanding forest ecosystem multifunctionality responses to various stand transformation methods remains limited. In this study, we assessed ecosystem multifunctionality, encompassing nutrient cycling, carbon stocks, water regulation, decomposition, wood production, and symbiosis, under different stand transformation methods (Chinese fir monoculture, mixed conifer and broad-leaf, broad-leaf mixed, and secondary forests). We also identified key factors contributing to variations in ecosystem multifunctionality. The results showed that Chinese fir plantations were more conducive to carbon stock creation, while broad-leaved mixed plantations excelled in water regulation. Secondary forests exhibited higher ecosystem multifunctionality than other plantation types, with Chinese fir plantations displaying the highest multifunctionality, significantly surpassing mixed coniferous and broad-leaved plantations. Our findings further revealed that soil nutrients and plant diversity have significant impacts on ecosystem multifunctionality. In summary, stand transformation profoundly influences ecosystem multifunctionality, and mixed plantations do not necessarily provide higher ecosystem multifunctionality than monoculture plantations.

Reduction in antimicrobial resistance in a watershed after closure of livestock farms.

Natural environments play a crucial role in transmission of antimicrobial resistance (AMR). Development of methods to manage antibiotic resistance genes (ARGs) in natural environments are usually limited to the laboratory or field scale, partially due to the complex dynamics of transmission between different environmental compartments. Here, we conducted a nine-year longitudinal profiling of ARGs at a watershed scale, and provide evidence that restrictions on livestock farms near water bodies significantly reduced riverine ARG abundance. Substantial reductions were revealed in the relative abundance of genes conferring resistance to aminoglycosides (42%), MLSB (36%), multidrug (55%), tetracyclines (53%), and other gene categories (59%). Additionally, improvements in water quality were observed, with distinct changes in concentrations of dissolved reactive phosphorus, ammonium, nitrite, pH, and dissolved oxygen. Antibiotic residues and other pharmaceuticals and personal care products (PPCPs) maintain at a similarly low level. Microbial source tracking demonstrates a significant decrease in swine fecal indicators, while human fecal pollution remains unchanged. These results suggest that the reduction in ARGs was due to a substantial reduction in input of antibiotic resistant bacteria and genes from animal excreta. Our findings highlight the watershed as a living laboratory for understanding the dynamics of AMR, and for evaluating the efficacy of environmental regulations, with implications for reducing environmental risks associated with AMR on a global scale.

[Distribution and Driving Mechanisms of Antibiotic Resistance Genes in Desert-Oasis Continuum].

The oasis agro-ecosystem is a complex ecosystem with intensive human activities in arid areas. Microbial antibiotic resistance is posing threats to human health and ecological balance. It is of great importance to investigate the diversity, distribution profiles, and driving factors of soil antibiotic resistance genes under different land use patterns in a desert-oasis continuum, especially for assessing soil environmental and human health risks in arid regions. In this study, high throughput sequencing combined with high throughput quantitative PCR were used to investigate the microbial community structure and patterns of antibiotic resistance genes in a desert-oasis continuum, aiming to explore the distribution characteristics and driving mechanisms of soil resistance genes. The results showed that the diversity and abundance of antibiotic resistance increased significantly from the edge of desert to the central oasis, along with Dest, Cotn, Maiz, Reed, and Sedt, consecutively, implying that farmland soil was an important reservoir of resistance genes, which was closely related to land use and land cover change. Soil microbial communities were significantly correlated with antibiotic resistance genes. Thiobacillus, Pontibacter, Nocardioides, Salinimicrobium, Solirubrobacter, and Streptomyces were important potential hosts of various resistance genes. The patterns of antibiotic resistance genes were shaped by heavy metal elements, MGEs, and microbial communities in arid soil, which accumulatively accounted for 70% of the variations in resistance genes alone or together and therefore drove the occurrence, enrichment, and evolution of resistance genes in agricultural soil of the desert-oasis continuum.

Manure and biochar have limited effect on lettuce leaf endophyte resistome.

Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.

City-scale distribution of airborne antibiotic resistance genes.

Concerns around urban air quality have been increasing worldwide due to large-scale urbanization. A large volume of work has been focused on the chemical pollutants in the air and their impacts on human health. However, the profile of airborne microbial contaminants, especially antibiotic resistance genes (ARGs), is largely understudied. Here, high-throughput quantitative PCR (HT-qPCR) was employed to explore the temporal and spatial distribution of airborne ARGs from 11 sites with various functional zones and different urbanization levels within Xiamen, China. A total of 104 unique ARGs and 23 mobile genetic elements (MGEs) were detected across all samples. Temporal shift was observed in the distribution of ARG profiles, with significantly higher relative abundance of ARGs detected in summer than that in spring. Temperature is the key predictor of the total relative abundance of ARGs and MGEs in summer, while PM2.5 and PM10 were the two most important factors affecting the abundance in spring. Our findings suggest that urban aerosols accommodate rich and dynamic ARGs and MGEs, and emphasize the role of temperature, air quality and anthropogenic activities in shaping the profile of ARGs.

Characterization of microbial community, ecological functions and antibiotic resistance in estuarine plastisphere.

The plastisphere is a new ecological niche. Compared to the surrounding water, microbial community composition associated with the plastisphere is known to differ with functional consequences. Here, this study characterized the bacterial and fungal communities associated with four types of plastisphere (polyethylene, polystyrene, polypropylene and polyvinyl chloride) in an estuarine habitat; assessed ecological functions including carbon, nitrogen, phosphorus and sulfur cycling, and determined the presence of antibiotic resistance genes (ARGs) and human pathogens. Stochastic processes dominated the community assembly of microorganisms on the plastisphere. Several functional genera related to nutrient cycling were enriched in the plastisphere. Compared to surrounding water and other plastisphere, the abundances of carbon, nitrogen and phosphorus cycling genes (cdaR, nosZ and chpy etc.) and ARGs (aadA2-1, cfa and catB8 etc.) were significantly increased in polyvinyl chloride plastisphere. In contrast, the polystyrene plastisphere was the preferred substrate for several pathogens being enriched with for example, Giardia lamblia 18S rRNA, Klebsiella pneumoniae phoE and Legionella spp. 23S rRNA. Overall, this study showed that different plastisphere had different effects on ecological functions and health risk in estuaries and emphasizes the importance of controlling plastic pollution in estuaries. Data from this study support global policy drivers that seek to reduce plastic pollution and offer insights into ecological functions in a new ecological niche of the Anthropocene.

Plants select antibiotic resistome in rhizosphere in early stage.

Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil.

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China.

Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p > 0.05) and the amylase gene abundance decreased firstly in middle-succession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling.