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This study investigated the effects of adding bile acids (BA) to the feed on several biological aspects of Yellow River carp (Cyprinus carpio). The experimental design covered four groups, namely, CT, BA1, BA2, and BA3, fed diets containing 0 mL/kg, 0.1 mL/kg, 1.0 mL/kg, and 10.0 mL/kg of BA, respectively, and the Yellow River carp with an initial body weight of 46.13±0.74 g were fed for 28 days. The results revealed that BA increased trypsin and lipase activities, positively influencing growth performance. Additionally, it enhanced the activity of intestinal antioxidant-related enzymes and the expression of related genes. Meanwhile, our findings suggested that the addition of BA might restrict hepatic lipid deposition by inhibiting lipogenesis-related genes and stimulating lipolysis-related genes. Furthermore, BA significantly altered the intestinal microorganisms' flora structure, leading to a decrease in the relative abundance of Proteobacteria.

ABSTRACTPlant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil–plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Abstract The use of microbial inoculant is a promising strategy to improve plant health, but their efficiency often faces challenges due to difficulties in successful microbial colonization in soil environments. To this end, the application of biostimulation products derived from microbes is expected to resolve these barriers via direct interactions with plants or soil pathogens. However, their effectiveness and mechanisms for promoting plant growth and disease resistance remain elusive. In this study, we showed that root irrigation with the extracts of Streptomyces ahygroscopicus strain 769 (S769) solid fermentation products significantly reduced watermelon Fusarium wilt disease incidence by 30% and increased the plant biomass by 150% at a fruiting stage in a continuous cropping field. S769 treatment led to substantial changes in both bacterial and fungal community compositions, and induced a highly interconnected microbial association network in the rhizosphere. The root transcriptome analysis further suggested that S769 treatment significantly improved the expression of the MAPK signalling pathway, plant hormone signal transduction and plant–pathogen interactions, particular those genes related to PR‐1 and ethylene, as well as genes associated with auxin production and reception. Together, our study provides mechanistic and empirical evidences for the biostimulation products benefiting plant health through coordinating plant and rhizosphere microbiome interaction.

Abstract Temporal lobe epilepsy (TLE) leads to extensive degradation of the quality of life of patients. Glycyrrhizic acid (GA) has been reported to exert neuroprotective effects on status epilepticus. Herein, the current study set out to explore the functional mechanism of GA in TLE young rats. Firstly, TLE young rat models were established using the lithium chloride and pilocarpine regimen and then subjected to treatment with different doses of GA, miR‐194‐5p‐antagomir, or/and sh‐prostaglandin‐endoperoxide synthase 2 (PTGS2) to observe changes in iron content, glutathione and malondialdehyde levels, and GPX4 (glutathione peroxidase 4) and PTGS2 protein levels in the hippocampus. Neuronal injury and apoptosis were assessed through HE, Nissl, and TUNEL staining. Additionally, the expression patterns of miR‐194‐5p were detected. The binding site of miR‐194‐5p and PTGS2 was verified with a dual‐luciferase assay. Briefly, different doses of GA (20, 40, and 60 mg/kg) reduced the epileptic score, frequency, and duration in TLE young rats, along with reductions in iron content, lipid peroxidation, neuronal injury, and apoptosis in the hippocampus. Silencing of miR‐194‐5p partly annulled the action of GA on inhibiting ferroptosis and attenuating neuronal injury in TLE young rats. Additionally, PTGS2 was validated as a target of miR‐194‐5p. GA inhibited ferroptosis and ameliorated neuronal injury in TLE young rats via the miR‐194‐5p/PTGS2 axis. Overall, our findings indicated that GA exerts protective effects on TLE young rats against neuronal injury by inhibiting ferroptosis through the miR‐194‐5p/PTGS2 axis.

Abstract Introduction Biological nitrogen (N) fixation (BNF) plays a key role in nitrogen supply in agricultural and natural ecosystems. Harnessing BNF can substantially reduce dependence on chemical fertilizer in agroecosystems and hence can contribute to sustainable agriculture. However, a number of field studies have demonstrated that BNF can be largely suppressed in phosphorus (P)‐deficient environments, while the underlying mechanism is not well understood. Materials & Methods In this study, comparative proteomics and lipidomics analyses were conducted on a diazotrophic bacterium Klebsiella variicola W12 under P‐deficient and P‐replete conditions to gain insight into how P availability affects N fixation. Results Under P deficiency, N fixation activity of K. variicola W12 was severely repressed. In response to P limitation, the bacterium synthesized P‐free ornithine lipids to replace glycerophospholipids in its membrane to reduce cellular demand for P. Comparative proteomics showed that P limitation resulted in upregulation of the PhoBR two‐component system, a range of organic and inorganic P uptake and transport systems, while nitrogenase and N‐fixation‐related transcriptional regulators NifL and NifA were downregulated. Conclusion These results revealed lipid renovation as an adaptation strategy for N2‐fixing microbes to survive under P stress and provided biochemical evidence on how P availability regulates BNF. A conceptual model of N–P coupling at the microbial metabolism level is therefore proposed. Our study provides a simple yet plausible explanation of how P deficiency suppresses BNF observed in the field and highlights the importance of regulating P availability to maximize the potential of BNF in agroecosystems for agriculture sustainable production.

Abstract Introduction Nitrification inhibitors and straw incorporation are used to reduce microbial mediated nitrogen (N) losses, thereby increasing N use efficiency (NUE) in cropland soil, but their effects on nitrous oxide (N2O) emission across different soil types and the underlying molecular mechanisms remain less understood. Materials and Methods In this study, we investigated how nitrification inhibitor nitrapyrin and straw incorporation affected soil N balance, N2O emission, nitrifiers and denitrifiers in three cropland soils (black, fluvo‐aquic and red soils). Results Compared with fertilization‐only treatment (N), nitrapyrin addition increased ammonium, while it decreased nitrate concentration in all soils; however, the performance of straw incorporation was less significant. Nitrapyrin decreased N2O emission only in the fluvo‐aquic soil, while straw incorporation strongly increased N2O emission in the red soil. Terminal restriction fragment length polymorphism analysis revealed that the denitrifier community was distinct across the three soils, but not strongly structured by nitrapyrin or straw incorporation. Compared with the N treatment, straw incorporation and nitrapyrin increased nosZ gene abundance only in the black soil. Structural equational modelling further confirmed that, after accounting for different soil properties, straw incorporation significantly increased N2O emission from black and red soils, and a decrease in nosZ gene abundance was the main biological factor for increased N2O emission in red soil. Conclusion Taken together, our work provides new knowledge that the performance of nitrification inhibitor and straw incorporation on N2O emission is soil type‐dependent, and management practices should be used as per soil type to balance NUE and N2O emission.

Abstract Background Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. Results Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. Conclusions The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.

Autophagy is responsible for maintaining fundamental cellular homeostasis and is, therefore, essential for diverse development processes. This study reported that PoElp3, the putative catalytic subunit of Elongator complex, is involved in the maintenance of autophagy homeostasis to facilitate asexual development and pathogenicity in the rice blast fungus Pyricularia oryzae. It was found that the ΔPoelp3 strains were defective in vegetative growth, conidiation, stress response, and pathogenicity. The mutants exhibited hyper-activated autophagy in the vegetative hyphae under both nutrient-rich and nutrient-deficient conditions. The hyper-activation of autophagy possibly suppressed the production of vegetative hyphae in the ΔPoelp3 strains. Moreover, the ΔPoelp3 strains were found to be more sensitive to rapamycin during vegetative- and invasive-hyphal growth but have no effect on Target-of-Rapamycin (TOR) signaling inhibition. Taken together, these results demonstrated that PoElp3 is involved in asexual development and pathogenicity by regulating autophagy in the rice blast fungus.

Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. Results Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. Conclusions Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract

Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.

Abstract Objective Resveratrol is a natural polyphenolic compound that ameliorates postmenopausal osteoporosis by activating the estrogen receptor. Research has shown that resveratrol exhibits some type of estrogen receptor agonist activity, reducing the risk of breast cancer. However, its mechanism of action remains largely unknown. This study aims to investigate the effect of resveratrol on osteoblastic and osteoclastic differentiation and its potential role in the regulation of autophagy. Methods Sprague Dawley (SD) rats underwent ovariectomies (OVX) and were administered resveratrol (at 10, 20 or 40 mg/kg/d) for 8 weeks. The calcium content and the bone mineral density (BMD) were measured in the lumbar vertebrae (L3) and the right distal femur-tibia bone region. The osteoblasts and osteoclasts were isolated from rat lumbar vertebrae by enzyme digestion and bone marrow induction, respectively. The cells were then cultured with resveratrol in combination with bafilomycin or leupeptin to inhibit or activate autophagy, respectively. Western blotting was used to assess the differentiation markers and autophagy-related genes in the osteoblasts and osteoclasts. Results Compared to the sham group, the bone calcium content and BMD were significantly decreased in the OVX group (p

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

Abstract Background Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

Abstract Nitrogen (N) fertilization has boosted grain production during the past century, while excess N fertilization with declining N use efficiency (NUE) has led to severe pollution in many regions. To achieve the goal of sustainable food production, Technologies and Management Practices (TMPs, e.g., optimum N application rate and methods, N‐transformation inhibitors) have been developed to improve crop yield and NUE and to reduce N losses. However, it remains unclear how N fate has been changed by environmental factors and TMPs. Here, we compiled a dataset of 366 field 15N tracer observations from 74 publications worldwide and conducted a meta‐analysis to examine how environmental conditions and management practices influence the fertilizer‐N fate one growing season after the fertilization of maize. We show that the proportion of 15N taken up by aboveground biomass (NUE15N), was significantly lower in China (33%) than that in North America (42%) and the European Union (54%). Soil organic carbon was the most critical environmental factor positively correlated with NUE15N. Among the nine selected categories of TMPs, deep placement of fertilizer and split application increased the grain yield and decreased the fertilizer‐N loss consistently among studies. Reducing the fertilizer‐N rate could increase the NUE15N but presents risks of yield reduction in some regions. This study demonstrates the importance of SOC and varying impacts of TMPs on the efficiency of fertilizer use in cropping systems globally and provides critical information for farmers and policymakers to improve N management for higher productivity and less pollution.

Abstract While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2 − µg−1 g−1 day−1, P

Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH4 and N2O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH4 and N2O emissions. However, little is known about their interactive effect on CH4 and N2O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH4 and N2O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH4 emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH4 emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N2O emissions at low input rate (S1) but significantly increased N2O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N2O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH4 and N2O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Background: Urination disorders are common in Parkinson′s disease (PD) and respond poorly to medication. This study aimed to analyze the risk factors for urination disorders in PD. Methods: Ninety-one patients with PD (aged 34-83 years old) were recruited. Patients were assessed with the Unified PD Rating Scale (UPDRS), Hoehn and Yahr stage, Pittsburgh Sleep Quality Index (PSQI), Hamilton Depression Rating Scale (HAMD), and Hamilton Anxiety Scale (HAMA). Micturition number was recorded, and Type B ultrasound was used to evaluate residual urine. Statistics was performed using binary logistic regression, bivariate correlations, and Chi-square and t-tests. Results: Of 91 patients, urinary dysfunction occurred in 55.0%. Among these, 49.5% suffered with nocturia, 47.3% with pollakiuria. Nocturia number had a positive linear relationship with HAMA score (odds ratio [OR] = 0.340, P = 0.001), HAMD score (OR = 0.323, P = 0.002), duration of L-dopa medication (OR = 0.328, P = 0.001), dose of L-dopa (OR = 0.273, P = 0.009), UPDRS-II (OR = 0.402, P = 0.000), UPDRS-III score (OR = 0.291, P = 0.005), and PSQI score (OR = 0.249, P = 0.017). Micturition number over 24 h was positively associated with HAMA (OR = 0.303, P = 0.004) and UPDRS-II scores (OR = 0.306, P = 0.003). Of patients with residual urine, 79.3% had a volume of residual urine

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0 to 44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8% to 93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 year and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (≥17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0 year to 5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities.

During the past decades, extensive nitrogen fertilization and acid deposition have greatly contributed to soil acidification in agroecosystems. Liming, the addition of calcium- and magnesium-rich material to soil, is an effective management strategy used to improve fertility and productivity of agricultural soils degraded by acidification. Nitrification plays a central role in nitrogen (N) availability in agroecosystems and contributes to soil acidification. However, little is known regarding the effects of liming on this process and microbial populations that drive it. Here, we investigated population dynamics and activity of ammonia oxidizers in response to a 2-year liming field trial in acidic soils received long-term fertilization with chemical N fertilizers and short-term lime amendment in microcosm incubations. Our results showed that activity, abundance and population structure of both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were sensitive to liming in fertilized acidic soils. AOB abundance and potential nitrification rates increased in field plots subjected to liming, whereas the opposite was observed for AOA. In microcosm incubations, AOA abundance increased progressively over 60 days, namely under low CaO levels, whereas AOB abundance was greatly stimulated only during the first week under high CaO levels. 13CO2-SIP-DNA experiments further supported that AOA were the most active ammonia oxidizers in fertilized field soils. However, in N-fertilized soils freshly amended with CaO, only autotrophic growth of AOB was observed after seven days, but not after 30 days when growth of AOA was observed. Taken together, our results indicated that both AOA and AOB play a role in nitrification following liming in fertilized acidic soils, likely through selection of better adapted clades of organisms. Although AOA were likely the main drivers of nitrification in these soils in the long-term, liming stimulated AOB activity in the short-term.