Soil Microbial Functional Genes Research Articles

Effect of Nitrogen Addition on Soil Microbial Functional Gene Abundance and Community Diversity in Permafrost Peatland.

Nitrogen is the limiting nutrient for plant growth in peatland ecosystems. Nitrogen addition significantly affects the plant biomass, diversity and community structure in peatlands. However, the response of belowground microbe to nitrogen addition in peatland ecosystems remains largely unknown. In this study, we performed long-term nitrogen addition experiments in a permafrost peatland in the northwest slope of the Great Xing’an Mountains. The four nitrogen addition treatments applied in this study were 0 g N·m−2·year−1 (CK), 6 g N·m−2·year−1 (N1), 12 g N·m−2·year−1 (N2), and 24 g N·m−2·year−1 (N3). Effects of nitrogen addition over a period of nine growing seasons on the soil microbial abundance and community diversity in permafrost peatland were analyzed. The results showed that the abundances of soil bacteria, fungi, archaea, nitrogen-cycling genes (nifH and b-amoA), and mcrA increased in N1, N2, and N3 treatments compared to CK. This indicated that nitrogen addition promoted microbial decomposition of soil organic matter, nitrogen fixation, ammonia oxidation, nitrification, and methane production. Moreover, nitrogen addition altered the microbial community composition. At the phylum level, the relative abundance of Proteobacteria increased significantly in the N2 treatment. However, the relative abundances of Actinobacteria and Verrucifera in the N2 treatment and Patescibacteria in the N1 treatment decreased significantly. The heatmap showed that the dominant order composition of soil bacteria in N1, N2, and N3 treatments and the CK treatment were different, and the dominant order composition of soil fungi in CK and N3 treatments were different. The N1 treatment showed a significant increase in the Ace and Chao indices of bacteria and Simpson index of fungi. The outcomes of this study suggest that nitrogen addition altered the soil microbial abundance, community structure, and diversity, affecting the soil microbial carbon and nitrogen cycling in permafrost peatland. The results are helpful to understand the microbial mediation on ecological processes in response to N addition.

Contrasting effects of warming and N deposition on soil microbial functional genes in a subtropical forest

Climate warming and nitrogen (N) deposition are expected to increase in the coming decades. The consequences of the interaction between warming and N deposition on forest ecosystems and their functions (i.e., carbon sequestration) remain uncertain. In this study, we examined the composition, diversities, and abundances of soil microbial functional genes in a subtropical forest after four years of exposure to warming and N addition. We found that warming alone did not have a significant effect on the composition, diversities, and abundances of functional genes, suggesting that four years were not long enough to reach the critical threshold that would activate a response to warming from soil functional genes in the subtropical forest. Conversely, warming significantly decreased soil labile carbon (C) content. The application of N in combination with warming significantly enhanced the diversities and abundances of functional genes associated with C and N cycling, leading to an accelerated loss of soil N. Interestingly, the interaction between warming and N addition did not have a significant effect on the diversities and abundances of functional genes associated with C and N cycling. Redundancy analysis indicated that a decrease in pH caused by N addition significantly affected the abundances of those functional genes. Overall, our study fills a research gap by examining the effect of simultaneous warming and N deposition on soil microbial functional genes in subtropical forests. Additionally, the study indicates that microbial functional genes are more sensitive to a combination of warming and N addition than to warming alone. Therefore, the effects of multi-factor global change on soil microbial functional genes cannot be underestimated.

Influence of tetracycline on arsenic mobilization and biotransformation in flooded soils

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0–50 mg kg−1) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

Variations in soil properties rather than functional gene abundances dominate soil phosphorus dynamics under short-term nitrogen input

Microorganisms play a vital role in regulating soil phosphorus (P) dynamics in terrestrial ecosystems. Here, we investigated the response of soil microbial P cycling potential traits to nitrogen (N) addition via metagenomics and the relationship between microbial potentials and soil P dynamics. Topsoil (0–10 cm) samples were collected from experimental soil that had been maintained for 3 years with low and high level of N addition in an alpine meadow of the Qinghai-Tibet Plateau. Soil microbial functional genes and P fractions were determined. The soil available P and microbial biomass P were significantly affected by N inputs and significantly associated with soil properties (including soil pH, alkaline phosphatase activity, and soil total N and NO3−-N contents). Meanwhile, high N input decreased the relative abundance of the pstS gene, and low N input reduced the relative abundances of phoB, ugpQ and C-P lyase genes. We further found that the pstS gene was a determinant of soil microbial biomass P and significantly correlated with soil pH. Moreover, Alphaproteobacteria with C-P lyase and Actinobacteria related to alkaline phosphatases and phosphate-specific transport were the most abundant taxa but not affected by N input. Short-term high N input could alter soil P dynamics and microbial functional genes. Although there were relationships between the pstS gene, microbial biomass P and soil pH, the microbial functional gene abundance was less important than soil properties in regulating soil P dynamics.

Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones.

Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.

The effects of nitrogen addition on soil organic carbon decomposition and microbial C-degradation functional genes abundance in a Pinus tabulaeformis forest

Nitrogen (N) deposition affects soil organic carbon (SOC) decomposition, therefore altering the global terrestrial carbon (C) cycle. However, it remains unclear how N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional gene composition. We investigated the effects of N addition (0, 3, 6, and 9 g N m−2y–1) on the composition of soil microbial C-cycling functional gene, SOC-degrading enzyme activities, and CO2 emissions in a Pinus tabulaeformis forest. Under low N addition (3 or 6 g N m−2y–1), labile C-degradation gene abundances were significantly increased. Under high N addition (9 g N m−2y–1), C-cycling functional gene abundance and diversity were significantly decreased. These effects were related to the changes in soil NO3–-N, dissolved organic C, total N, and microbial biomass C contents. Furthermore, low N addition stimulated the activities of SOC-degrading enzyme and CO2 emissions, whereas high N addition had the inhibitory effect. C-degradation gene abundances were significantly correlated with the SOC-degrading enzyme activities and CO2 emissions. Increase in CO2 emission rates were related to the high microbial functional potentials for labile C degradation under low N addition, whereas the lower CO2 emission rates were related to the low microbial functional potentials for labile as well as recalcitrant C degradation under high N addition. Our study indicated that N deposition may change SOC decomposition by altering the abundance of labile C and recalcitrant C degradation genes.

A latitudinal gradient of microbial β‐diversity in continental paddy soils

AbstractAimThe β‐diversity of plants and animals generally decreases with increasing latitudes. Here, we tested whether this relationship also holds for soil microbes at both functional and taxonomic levels.LocationChina.Time periodBetween June and October 2013.Major taxa studiedSoil archaea, bacteria, and functional genes.MethodsWe used a spatially explicit ‘L‐shaped’ sampling strategy in 39 paddy fields in China to study the pattern of soil microbial β‐diversity (i.e., species turnover, βz) across a latitudinal gradient (19.75° N to 47.58° N), with 11 soil samples taken within a 100 m × 100 m plot from each field. Archaeal and bacterial communities were analysed by sequencing 16S ribosomal RNA gene amplicons using Illumina MiSeq; microbial functional genes involved in C/N/P/S cycling were detected by GeoChip.ResultsWe showed that the microbial β‐diversity varied considerably across taxonomic and functional groups. For both soil microbial communities and functional genes, β‐diversity decreased significantly along elevated latitudes at the continental scale. Woesearchaeota of archaeal communities, Bacteroidetes of bacterial communities, and the functional genes involved in methane production displayed the greatest decreases. Both mean temperature during the growing season of rice plants and paddy soil heterogeneity contributed to the latitudinal patterns. Further analyses indicated that temperature was more important than soil heterogeneity in driving the β‐diversity of microbial communities and functional genes.Main conclusionsThese results highlight the importance of temperature‐driven soil microbial β‐diversity and suggest the potential to predict the changes of microbial diversity with climate change.

Land-use change from cropland to plantations affects the abundance of nitrogen cycle-related microorganisms and genes in the Loess Plateau of China

The “Grain for Green” project has been considered an effective avenue to control soil erosion, improve vegetation coverage and prevent ecosystem degradation in the Loess Plateau of China. However, the effect of the project on the underlying microbial mechanism of soil nitrogen cycling is not well understood. In the present study, the effect of land-use change from cropland to plantations on soil microbial community and functional genes involved in the nitrogen cycle was investigated via metagenomic sequencing analyses. The abundance rather than the composition of functional genes for nitrification, denitrification, assimilatory and dissimilatory nitrogen reduction significantly changed during the conversion of cropland to plantations. The abundance rather than the composition of microorganisms involved in the nitrogen cycle also changed significantly. The effect on the abundance of functional genes and microorganisms was mainly related to changes in soil properties, such as organic matter, total nitrogen, available phosphorus, available potassium and pH. The observed changes likely decrease the potential of nitrification, denitrification and assimilatory nitrogen reduction in the soil of plantations. Our results demonstrate that land-use change from cropland to plantations significantly affects soil nitrogen cycling in the Loess Plateau of China.

长白山林线过渡带树岛土壤微生物群落结构和生态功能

林线过渡带是指从郁闭森林上限到树种分布上限之间的区域，过渡带内生物多样性丰富，生态系统结构、功能和生态过程在很小的海拔梯度内发生剧烈变化，因此对全球气候变化和人类活动极为敏感。树岛是在林线过渡带内出现的斑块状或条带形不连续分布的树木集群，树岛内生存的树木通常能达到与较低海拔郁闭森林同样的高度和胸径，因此揭示树岛这一特殊生境的生态特征及其形成机制，对于预测未来气候变化下林线动态具有重要意义。以长白山岳桦林线过渡带一大型树岛作为研究对象，测定了土壤理化性质和土壤酶活性，采用宏基因组测序技术分析了微生物群落结构组成和功能基因丰度，通过与同海拔的开阔区生境进行对比，揭示了树岛这一特殊生境的土壤微生物群落结构特征和潜在生态功能，从土壤养分和土壤微生物学角度，阐明树岛形成的可能驱动机制。结果表明，树岛土壤的含水量、总碳、总氮和微生物生物量显著高于同海拔开阔区（P<0.05），与微生物r-策略相关的生理生化和遗传学指标，包括纤维素酶活性、放线菌相对丰度、与转录、防御、控制细胞周期相关的基因丰度、小分子碳降解基因丰度，均高于开阔区（P<0.05）。相反的，与微生物K-策略相关的指标，包括酸杆菌相对丰度、大分子碳降解基因相对丰度低于开阔区。揭示了树岛土壤微生物学特征，并从土壤微生物组学角度探讨了树岛形成的潜在机制，认为树岛内土壤养分增加并导致微生物群落r-策略倾向，这种变化反过来也可能促进树岛进一步扩大，进而影响林线动态。;The transition from the uppermost closed tall forests to the tree species line is often called the treeline ecotone. The treeline ecotone is one of the most important climate driven ecological boundaries and a potential habitat for diverse plant species. The ecosystem structure, function and ecological process can change over short elevational gradient in this specific habitat, and thus, the treeline ecotone ecosystem is thought to be extremely vulnerable to global climate change. The tree island is characterized by clumped patches or linear strips of krummholz or trees above the continuous forest limit. The trees in the tree island can sometimes grow to a relatively large size, with similar tree height and diameter breast height to the trees in the closed forest. To reveal the ecological characteristics and formation process of the specific habitat is of great significance in predicting the treeline dynamics under future climate change scenario. Research of the treeline ecotone has mostly focused on the aboveground vegetation cover. In this paper, soil samples were collected at the treeline ecotone of the birch forest line in the north slope of Changbai Mountain, within the tree island and the open area located at the same altitude, respectively. Soil physicochemical properties and enzymatic activities were measured. Soil microbial community structure and functional genes were analyzed by shot-gun metagenomic sequencing. The results showed that the soil moisture content, total carbon, total nitrogen and microbial biomass of the tree island were significantly higher than those of the open area (P<0.05). The microbial r-strategy indicators, including cellulase activity, relative abundance of Actinobacteria, gene abundance related to transcription, defense mechanisms, cell cycle control, cell division, chromosome partitioning and simple carbon compounds degradation, were much higher in the tree island than those in the open area. On the contrary, the indicators related to the microbial K-strategy, including the relative abundance of Acidobacteria and the abundance of complex carbon compounds degradation genes, were higher in the open area. The study, for the first time, explores the microbial community structure and ecological function in a tree island ecosystem, and explains the mechanisms of tree island formation based on microbial genomic data. We proposed that the soil nutrients were enriched, and the microbial community was shifted towards r-strategy in tree island. The changes in soil nutrients and microbes would in turn regulate the tree growth and thus might enlarge the tree island area and influence the dynamics of treeline.

Salinity controls soil microbial community structure and function in coastal estuarine wetlands.

Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha−1 year−1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha−1 year−1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha−1 year−1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha−1 year−1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH4+, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO2−/NH4+ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.

Grazing promoted soil microbial functional genes for regulating C and N cycling in alpine meadow of the Qinghai-Tibetan Plateau

Microbial functional genes can reflect the nutrient cycle activities in soil, because they encode various enzymes involved in the material cycle. Therefore, the gene abundance variation can reveal the impact of interference on the material cycle of grassland. To study the cycle of carbon (C), nitrogen (N) and phosphorus (P) between plant and soil in grassland under different grazing regimes, we investigated the soil microbial functional genes related to C, N, and P cycling by high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis under grazing exclusion (GE), rotational grazing (RG), and continuous grazing (CG) in alpine meadow of the Qinghai-Tibetan Plateau, where climate is characterized by little rain and low temperature, and grassland is very sensitive to grazing. The results showed at the early grazing period, C fixtion (rbcL, korA, and frdA) and lignin degradation (abfA, xylA, exg, lig, exoPG, chiA, and glx) processes were slower under GE; CH4 metabolism (mcrA) was faster under CG; RG and CG improved the denitrification process (narG); RG slowed down organic-P mineralization (phoD). At the late grazing period, C fixation (accA and frdA) and degradation (mnp, apu, and amyA) processes were slower under GE; CH4 metabolism (pmoA and mxa) was faster under CG; RG and CG improved the ammonia-oxidizing (amoA2), nitrification (hao), and denitrification (nirS3 and nirK1) processes. The majority of the genes involved in C, N, and P cycling decreased, the C, N and P content in plant leaf decreased, while that of soil increased from early to late grazing period. No matter grazing or not, there were negative relationships between genes and soil nutrients, and positive relationships between genes and plant nutrients, implying a trade-off between plant nutrients and soil nutrients along the grazing time. The genes responsible for regulating C and N cycling were increased under grazing, implying that reasonable grazing is beneficial to the nutrients cycling of grassland.

Application of biogas slurry rather than biochar increases soil microbial functional gene signal intensity and diversity in a poplar plantation

Microbes play critical roles in the cycling of nutrients in forest ecosystems. Many studies have shown that the application of organic fertilizer can alter bacterial diversity; however, the responses of soil microbial functional genes to organic fertilization (particularly biogas slurry fertilization, or in combination with biochar) have not been elucidated as yet. We examined the responses of the abundance, diversity, and composition of soil microbial functional genes under five-years of fertilization. This fertilization involved low and high application rates of biogas slurry, at 250 and 375 m3 ha−1 yr−1, respectively, or in combination with low and high application rates of biochar, at 80 and 120 t ha−1, respectively, in a coastal poplar plantation of Eastern China. Compared to the control, the normalized signal intensity of genes in the major functional categories increased significantly in response to the quantity of applied biogas slurry, but insignificantly in response to the additional application of biochar. Subsequent to the application of biogas slurry, the functional gene evenness and Shannon index increased significantly; however, the addition of biochar to the biogas slurry had insignificant effects on the α-diversity of functional genes. These functional gene compositions under five different treatments were well distinguished, primarily through the application of biogas slurry. Our results revealed that the abundance of a large number of key functional genes involved in C, N, and P cycling were effectively increased, and these changes were well correlated with most soil properties. This study reveals the molecular level mechanisms that promote plant growth following organic fertilizer application, through the enhancement of soil microbial functional gene diversity.

The responses of soil nitrogen transformation to nitrogen addition are mainly related to the changes in functional gene relative abundance in artificial Pinus tabulaeformis forests

The increase of soil nitrogen (N) availability may alter soil microbial community composition and the natural N cycle in forest ecosystems. However, the responses of soil microbial nitrogen functional genes (NFGs) to N addition and their consequent effect on the N-cycle processes are poorly understood. In this study, soil samples were collected from an artificial Pinus tabulaeformis forest located in Loess Plateau (China) to which N at four different concentrations was added (0 [N0], 3 [N3], 6 [N6], and 9 [N9] g N m−2 y−1) for 4 years. We quantified the relative abundance of NFGs using functional gene microarray GeoChip 5.0 and determined net N transformation and N2O emission rates in a 14-day incubation experiment. The results showed that N3 and N6 treatments did not significantly affect the total relative abundance and diversity of NFGs assemblage but significantly increased the relative abundance of specific genes for the NH3 cycle (ureC, nirA, and nrfA), and nitrification (amoA) and denitrification (norB). These positive effects were related to the increase in soil organic C, NO3−-N, and microbial biomass C (MBC). N9 treatment significantly decreased the relative abundance of all NFGs, and this negative impact was correlated with reduced dissolved organic C and MBC. Moreover, N addition significantly changed net N nitrification, mineralization, and N2O emission rates, and NFGs explained the higher variances in the N transformation processes than soil properties. Specifically, ammonia-oxidizing archaea (amoA-AOB) and MBC were the key factors related to net N nitrification; ureC, nirK, and MBC were the key factors related to net N mineralization; and narG and nirS were the key factors related to N2O emission. Our results show that global N deposition may mainly influence N transformation processes by regulating the corresponding NFG relative abundance, thereby affecting the N cycle in forest soils.

Effects of biochar on soil microbial community and functional genes of a landfill cover three years after ecological restoration

Landfills, as the most common approach to disposing of municipal solid waste worldwide, disturb native ecosystems and create a need for ecological restoration. The restoration of landfill cover with biochar has shown immediate potential to improve soil microbial functions within one year. However, such characteristics could change after a longer period of time. Here, soil properties, microbial communities, and microbial functional genes related to nutrient cycling were investigated three years after the biochar amendment of the topsoil of a subtropical landfill cover. The results showed that the levels of soil organic matter, water content, total carbon (C), total nitrogen (N) and total phosphorus (P) of biochar-amended soils were higher than those of control soil. Different soil microbial community structures were observed in the biochar-amended and control soils. Nine phyla, including Proteobacteria and Acidobacteria, but not Actinobacteria or Chloroflexi, were enriched in the biochar-amended soil. Although the impact of biochar on shaping microbial communities increased after a longer period of restoration, no differences were observed in soils that were amended using different biochar:soil ratios. The abundances of functional genes related to C and N cycling decreased, whereas those of genes related to P cycling were higher in soils that received biochar amendment. This finding suggests that compared with the control soil, biochar-amended soils were less active in processes involved in C and N cycling but enhanced in processes related to P cycling. This study can serve as a reference for future ecological restoration of degraded lands using biochar.

The diversity of microbial community and function varied in response to different agricultural residues composting.

Microbial activities are the dynamic core in the soil nutrient cycle. To improve the knowledges about the responses of soil microbial community structure and potential function to long-term cover crops practice. The co-occurrence patterns of soil microbial community structure and functional genes were evaluated using 16SrRNA, ITS and metagenomic technique in 13years cover crops of orchard grass (OG, Dactylis glomerata L.) with high C/N and white clover (WC, Trifolium repens L.) with low C/N. Conventional tillage (CT) was control. The experiment was implemented in an apple orchard located on the Loess Plateau, China, from 2006 to 2018. We also measured soil physicochemical properties and enzyme activities related to carbon and nitrogen cycling. The conclusions showed that the dominant bacterial phyla were Actinobacteria 27.68% in OG treatment and Proteobacteria 25.89% in WC treatment. Organic matter inputs stimulated growth of the phyla of Actinobacteria, Firmicutes, Chloroflexi, Ascomycota and genera of Bacillus, Blastococcus, Streptomyces and Penicillium. Interestingly, the OG and WC treatments promoted the fungal and bacterial alpha-diversity compared to CT treatment, respectively. In addition, compared to CT treatment, OG treatment was beneficial to the increase of C-cycle enzyme activity, while WC treatment tended to increase the N-cycle enzyme activity. Notably, compared to CT treatment, they both enriched carbon fixation and cycle pathways genes, while WC treatment increased the nitrogen metabolism pathway genes. Moreover, OG treatment was more conducive to the enrichment of carbohydrate enzymes genes involved in the hydrolysis of cellulose and hemicellulose compared to WC treatment. Overall, different quality of plant residues stimulated the specific expressions of soil microbial community structure and function. Long-term planted white clover was effective strategy to improve soil quality.

Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands

Despite distinct roles of soil microbes in regulating carbon (C) respiration in diverse environments, it remains unclear whether microbial taxonomic and functional attributes can consistently predict soil C emissions across contrasting ecosystems. Here, we conducted a large-scale sampling event across two contrasting croplands (rice and wheat-corn crop rotation) to identify specific soil microbial phylotypes and functional genes associated with soil respiration rates. The results of structural equation modeling indicated that bacterial community composition had a strong link with C respiration rates in the two contrasting cropland types; however, this link was weaker for fungal communities. More importantly, we found that the relative abundances of bacterial Solirubrobacterales_480-2, Myxococcales_mle1-27 and fungal Westerdykella had consistently negative correlation with respiration rates across paddy and upland soils. We also identified taxa that are significantly correlated to C respiration in the paddy (e.g. Methylocaldum) and upland soils (e.g. Kribbella), respectively. Further, we found multiple associations between functional genes involved in microbial C metabolism and soil respiration rates. Our findings provide novel insights into understanding microbial predictors of soil CO2 emissions in diverse croplands, which have important implications for improving C emission predictions in terrestrial ecosystems.

Differential responses of soil N2O to biochar depend on the predominant microbial pathway

Biochar amendment has been proposed as a potential strategy to reduce soil nitrous oxide (N2O) emissions, although experimental studies have generated inconsistent results on N2O emissions following biochar amendment. Differential responses of soil N2O to biochar amendment may depend on soil microbial functional genes abundance and abiotic properties. Here we sampled three types of soil from fields under long-term cultivation of green tea (TG), film greenhouse vegetable cabbage (GV) and Jerusalem artichoke (JA), respectively. We conducted a microcosm experiment to examine N2O emissions from the different soils following biochar amendment. Results showed that biochar amendment increased N2O emissions from the GV soil while decreasing N2O emissions from the TG and JA soils in the presence of nitrogen fertilizer. Biochar amendment increased soil pH and C/N ratio across the three soils. Quantitative PCR (qPCR) analysis showed that biochar amendment also consistently increased the abundances of AOB and nosZ genes but decreased the AOA abundances for all the soils, while the effects of biochar on the abundances of nirK and nirS genes differed between the soils. Our results suggest that biochar amendment can affect the processes of both ammonia oxidation and reduction of N2O to N2 for all the soils and the net effect of biochar on N2O emissions depended on the predominant process in a specific soil. Biochar-induced increase in N2O emissions in the GV soil was largely attributed to the stimulated nitrification rate, which was primarily driven by AOB. Biochar-induced decreases in N2O emissions in the TG and JA soils were linked to the increased nosZ gene abundances. Overall, the effectiveness of biochar for mitigating N2O emissions is linked to its dominant N2O production pathway in soils.

Microbial Community Structures and Important Associations Between Soil Nutrients and the Responses of Specific Taxa to Rice-Frog Cultivation.

Rice-frog cultivation is a traditional farming system in China and has been reintroduced as an agricultural practice in China in recent years. The microbial community in paddy rhizospheric soils has attracted much attention because many microorganisms participate in functional processes in soils. In this study, Illumina MiSeq sequencing-based techniques were used to investigate soil microbial communities and functional gene patterns across samples obtained by conventional rice cultivation (CR) and rice-frog cultivation (RF). The results showed that RF significantly affected the microbial community composition and richness, which indicated that the rhizospheric microorganisms responded to the introduction of tiger frogs into the paddy fields. Operational taxonomic units (OTUs) from Sandaracinaceae, Anaerolineaceae, Candidatus Nitrososphaera, Candidatus Nitrosotalea, Candidatus Nitrosoarchaeum and some unclassified OTUs from Euryarchaeota and Agaricomycetes were significantly enriched by RF. The abiotic parameters soil organic carbon (SOC), nitrate nitrogen (NO3−-N), and available phosphorus (AP) changed under RF treatment and played essential roles in establishing the soil bacterial, archaeal, and fungal compositions. Correlations between environmental factors and microbial communities were described using network analysis. SOC was strongly correlated with Anaerolineaceae, Methanosaeta, and Scutellinia. NO3−-N showed strong positive correlations with Opitutus, Geobacter, and Methanosaeta. NH4+-N was strongly positively associated with Sideroxydans, and TN was strongly positively correlated with Candidatus Nitrotoga. Compared to conventional CR, RF greatly enriched specific microbial taxa. These taxa may be involved in the decomposition of complex organic matter and the transformation of soil nutrients, thus promoting plant growth by improving nutrient cycling. The unique patterns of microbial taxonomic and functional composition in soil profiles suggested functional redundancy in these paddy soils. RF could significantly affect the bacterial, archaeal, and fungal communities though changing SOC and AP levels.

Changes in soil properties rather than functional gene abundance control carbon and nitrogen mineralization rates during long-term natural revegetation

Agricultural abandonment has been taken as one of the most widely used strategies for ecological restoration. Abandoned croplands expanded worldwide since the middle of the twentieth century and will increase considerably in the future. Whether agricultural abandonment alters the abundances of soil carbon (C) and nitrogen (N) mineralization genes, and whether these functional genes are linked to alterations in C and N mineralization rates remain unknown. We took advantage of a well-established chronosequence of nature restoration sites on abandoned croplands which represent a century of vegetation succession in China’s Qinling Mountains, to determine soil C and N mineralization rates, and their relationships with vegetation succession, edaphic characteristics, soil microbial communities, and functional genes based on GeoChip 5.0. We found that soil C and N mineralization rates, microbial biomass and composition, and the number and abundances of functional genes were significantly affected by vegetation succession following agricultural abandonment. Soil C and N mineralization rates increased by sixfold and threefold, respectively, along the cropland to forest successional gradient. The NO3-N, NH4-N and soil available phosphorus (P) concentrations were important factors associated with the C and N mineralization genes. The shifts in edaphic environments (i.e., soil moisture, cation exchange capacity, and C/P ratio), vegetation-derived substrates (i.e., soil organic C and N), and soil microbial composition (i.e., Fungi/Bacteria ratio, amounts of Gram-negative bacteria, Actinomycetes, and arbuscular mycorrhizal fungi), rather than the abundances of functional genes involved in mineralization processes, controlled soil C and N mineralization rates along the long-term vegetation successional gradient. Abandoning cropland for natural succession could facilitate the recuperation of soil C and N processes and alter soil microbial composition and functional genes. The abundances of microbial functional genes are less important than previously expected in regulating soil C and N mineralization rates.