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Soil disease-suppressiveness depends on complex interactions among pathogens, native microbiota, and physicochemical properties, while these interactions remain understudied. Comparing field and microcosm experiments, we investigated the significance of these interactions in disease emergence or suppression using structural equation modelling (SEM) and receiver operating characteristic curve (ROC) analyses. We observed significant differences in the relative abundance of pathogenic and beneficial microbes, alpha and beta diversity indices between disease-conducive and -suppressive rhizosphere soils. The pathogenic (Ralstonia) and beneficial (Bacillus) taxa dominated disease-conducive and -suppressive rhizosphere soils, respectively. Moreover, the co-occurrences of Ralstonia with native microorganisms were positive and negative in the disease-conducive and -suppressive soils, respectively. These results suggest the supportive (Rudaea) and suppressive (Enterobacter, Bacillus) role of indigenous microbes in the invasion of soil and plant systems by Ralstonia. The SEM and ROC analysis predicted that Ralstonia invaded rhizospheric microbial networks and caused peanut wilt under high than low soil phosphorus conditions. Our results suggest the importance of soil phosphorus availability in altering the microbial interactions, thus leading to soil invasion by Ralstonia. Thus, we conclude by saying that feeding soil with high amounts of available phosphorus could deplete plant-beneficial microbes and increase the pathobiome abundance that may compromise plant health.

Understanding the chemical composition and molecular transformation in soil dissolved organic matter (DOM) is important to the global carbon cycle. To address this issue, ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) was applied to investigate DOM molecules in 36 paddy soils collected from subtropical China. All the detected 7576 unique molecules were divided into seven compound groups, and nine trade-off relationships between different compound groups were revealed based on principal component analysis and Pearson's correlation. An optimized method was developed to evaluate all potential molecular transformations in DOM samples. The concept of thermodynamics was introduced to evaluate the identified molecular transformations and classify them as thermodynamically favorable (TFP) and thermodynamically limited (TLP) processes. Here, we first tried to understand the molecular trade-offs by using the potential molecular transformations. All the nine trade-offs could be explained by molecular transformations. Six trade-offs had bases of biochemical reactions, and the trade-off-related direct transformations could explain the content variations of carbohydrate-like, condensed aromatic-like, tannin-like, and lignin-like compounds in TLP. More reasonable explanations existed in the TLP rather than TFP, which demonstrated the critical role of external energy in the molecular transformation of soil DOM.

Harnessing the rhizobia-legume symbiosis is a promising strategy to confront sustainability in agriculture. Agricultural research on legume nodulation has mostly focused on abiotic parameters, yet the importance of biotic variables on legumes nodulation is still ambiguous. We explored the variation of bacterial communities in peanut rhizosphere soil under different agricultural practices (peanut fallow rotation and Vicia villosa Roth-peanut rotation) using Illumina sequencing. Samples were collected in 2020 from a 9-year study (2012–2020) located at Dongxiang countryside (Jiangxi province, China). Compared with peanut fallow rotation (PFR), Vicia villosa Roth-peanut rotation (VPR) significantly (p< 0.05) decreased soil pH (by 0.4–3.9%) and number of peanut nodules (by 20–63.7%). By using the Random forest tool, we found that the difference in peanut nodulation was associated with specific microbiome alterations. The indicator taxa positively responded to the peanut nodulation was enriched in the PFR practice, while VPR led to increased abundance of indicator taxa which negatively responded to peanut nodulation. The path analysis indicated that soil pH has an indirect effect on peanut nodulation through its link with the abundance of indicator taxa. Our work provides evidence that the variation in peanut rhizosphere microbial communities was associated with peanut nodulation.

There have been many studies about the effects of long-term fertilizations on crop yields and soil organic carbon. However, little attention has been paid to the response of soil dissolved organic carbon (DOC) to fertilization practices. The aims of this work were to investigate the variations of the content and the chemical composition of soil DOC under long-term different fertilizations and to evaluate their correlations with maize yields. A long-term fertilization experiment under a double maize cropping system was established in 1986 in acidic Ultisols of southern China. Soil samples were collected in April 2014 from the following ten treatments: (1) CK (non-fertilization), (2) N (only N fertilization), (3) P (only P fertilization), (4) K (only K fertilization), (5) NP (N and P fertilization), (6) NK (N and K fertilization), (7) NPK (N, P, and K fertilization), (8) HNPK (double doses of NPK fertilization amount), (9) OM (only organic manure), and (10) NPKM (NPK fertilization plus organic manure). The soil basic chemical properties including the content of DOC were determined. Then, the chemical composition of soil DOC was assessed through three-dimensional excitation-emission matrix (3DEEM) and parallel factor analysis (PARAFAC). The results showed that long-term application of organic manure significantly increased the content of soil DOC and obviously changed the chemical composition of soil DOC. Based on the 3DEEM and PARAFAC, organic manure treatments (OM, NPKM) had higher proportions of tryptophan-like components and lower proportions of tyrosine-like components as compared with other treatments (CK and inorganic fertilizer treatments). For the fluorescence indices, organic manure treatments showed significantly higher humification index (HIX) and lower biological index (BIX) and McKnight index than other treatments. Aggregated boosted trees analysis revealed that the DOC content explained 24.6% of the total variance in maize yields and ranked first among all tested soil chemical properties. Furthermore, all fluorescence properties of DOC were correlated with maize yields, in which the HIX index was the most important factor. This research demonstrated that not only the content of DOC but also the chemical composition of DOC in acidic Ultisols were significantly correlated to maize yields. It may be an effective way to improve soil quality and productivity by increasing DOC content and HIX index. From the perspective of soil DOC, our results proved again that application of organic manure could be the most suitable fertilization practice in acidic Ultisols of southern China.

The evolution of increased competitive ability (EICA) hypothesis states that, when introduced in a novel habitat, invasive species may reallocate resources from costly quantitative defense mechanisms against enemies to dispersal and reproduction; meanwhile, the refinement of EICA suggests that concentrations of toxins used for qualitative defense against generalist herbivores may increase. Previous studies considered that only few genotypes were introduced to the new range, whereas most studies to test the EICA (or the refinement of EICA) hypotheses did not consider founder effects. In this study, genetic and phenotypic data of Chromolaena odorata populations sampled across native and introduced ranges were combined to investigate the role of postintroduction evolution in the successful invasion of C. odorata. Compared with native populations, the introduced populations exhibited lower levels of genetic diversity. Moreover, different founder effects events were interpreted as the main cause of the genetic structure observed in introduced ranges. Three Florida, two Trinidad, and two Puerto Rico populations may have been the sources of the invasive C. odorata in Asia. When in free of competition conditions, C. odorata plants from introduced ranges perform better than those from native ranges at high nutrient supply but not at low nutrient level. The differences in performance due to competition were significantly greater for C. odorata plants from the native range than those from the introduced range at both nutrient levels. Moreover, the differences in performance by competition were significantly greater for putative source populations than for invasive populations. Quantities of three types of secondary compounds in leaves of invasive C. odorata populations were significantly higher than those in putative source populations. These results provide more accurate evidence that the competitive ability of the introduced C. odorata is increased with postintroduction evolution.

Understanding microbial community succession is key to uncover the mechanisms driving variation in soil fertility under rice cultivation. To evaluate microbial community divergence along paddy soils after 9, 15 and 25 years of cultivation with and without intensive fertilization, 16S rRNA gene high throughput sequencing and network co-occurrence analysis were used. Except for the initial barren soil, three different fertilization treatments were applied to rice planted soil: control (CK, without fertilization), NPK (N + P + K), and NPKM (NPK plus manure). Fertilization increased the difference of microbial species abundance between rice paddy soil and the initial barren soil reflecting higher C input by roots under fertilization. The bacterial communities after 9 and 15 years of rice cultivation clustered together and differed from those in barren soil and after 25 years of rice cultivation. Oligotrophic bacterial groups in the fertilized soil were gradually substituted with copiotrophic microorganisms during rice cultivation. The redundancy analysis indicated that the divergence in the microbial community structure during rice cultivation increased with soil organic C and total N. The network co-occurrence analysis showed that microbial network in NPKM soil contained the largest ratio of positive to negative links, whereas the CK network contained the smallest. Hence, fertilization and its duration control the distribution of keystone species and the nature of the links established between them.

Methanogenesis is crucial in the carbon cycle, and conductive iron oxide minerals play an important role in methanogenesis in anoxic environments. The influence of iron oxides is ubiquitous, but the strength and nature of iron oxides effects are believed to vary in response to environmental conditions, especially the soil iron concentration. We evaluated the influence of conductive nanoFe3O4 on straw degradation in high-iron (HR) and low-iron (LR) paddy soil enrichments, as well as the corresponding responses of related microorganisms. Under conductive nanoFe3O4 amendment, methane production and straw degradation increased by 184%–285% and 7.8%–12.7%, respectively, in the two soil enrichments. The increase apparently coincided with increased interspecies interactions within the microorganismal community, especially enhanced syntrophic cooperation among fermenting bacteria, syntrophic bacteria and methanogenic archaea, and facilitated interspecies electron transfer, which improved carbon conversion and alleviated end-product inhibition. The methanogenic archaeal community also exhibited changes with nanoFe3O4 amendment, and the relative abundance of Methanosarcina increased. Pairwise comparisons revealed that although methanogenic straw degradation was higher in HR soil than in LR soil, the enhancement induced by the nanoFe3O4 amendment showed to a larger degree and the microbial responses were more distinct in LR soil than in HR soil. The abundances of Geobacter and Methanosarcina greatly increased, and the microbial community shifted towards a composition similar to that in HR soil. This work indicates that iron oxides facilitate the methanogenic degradation of rice straw and that the indigenous iron content significantly influences the microbial community composition. This study provides a technique for agricultural residue degradation and has clear implications for our understanding of soil C-Fe biogeochemical coupling.

BACKGROUND: Humic‐like substances (HULIS) for use in controlling soil‐borne diseases have been a research focus, but obtaining HULIS with high fungistatic activity via different extraction solvents has been challenging. In this work, three solvents were selected to extract HULIS from weathered coal. Inhibition rates against phytopathogens were used to evaluate the fungistatic activities of HULIS. Element contents (C, N, S, and O) and carbon‐13‐cross polarization magic‐angle spinning nuclear magnetic resonance (¹³C‐CP‐MAS NMR) spectra were used to evaluate the chemical composition. The relationships between the chemical compositions and fungistatic activities were assessed by redundancy analysis (RDA) and partial least squares regression (PLSR). RESULTS: The results showed that HULIS extracted with different solvents varied in the element contents, organic carbon structures and fungistatic activities. HULIS extracted with potassium hydroxide–ethanol had the highest content of C, the lowest contents of N and O, and the highest fungistatic activities (up to 71.86%). Consistent results through RDA and PLSR shows that C and S had positive effects on the fungistatic activity, while N and O had negative effects. Aliphatic C in HULIS had positive effects on the fungistatic activity, while the aromatic fraction and anomeric C had negative effects. CONCLUSION: In summary, different solvents extracted different fractions from weather coal. Mixed solvents with organic and inorganic solvents were more beneficial for extracting active fractions with higher fungistatic activity of HULIS from weather coal. The results of this work provide a good theoretical basis for the application of HULIS extracted from weathered coal. © 2019 Society of Chemical Industry

Background Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with 13CO2, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP). Results Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem. Conclusions Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems.

Sequestration of soil carbon is considered as a promising strategy for mitigating climate change. As a source of recalcitrant carbon, biochar has been widely used in agricultural soil as a mean of stabilizing soil organic carbon (SOC). However, limited reports focused on the changes of biochar itself in soil when compared with the bulk SOC after biochar addition. To explore how environmental conditions influence the stability of biochar, isolated straw-derived biochar particles (0.25-2 mm) were embedded in an Anthrosol for 12 months under varied environmental conditions of incubation temperature (15 °C, 25 °C and 35 °C) and moisture (60 % and 150 % of saturated water content). Within the early 1 month of incubation, pH and inorganic nitrogen contents of biochar changed significantly as a function of moisture and temperature (p0.01), whereas water extractable organic carbon (WEOC) content was only influenced by moisture content (p0.01). The highest temperature (35 °C) and saturated water content (150 %) induced the largest aging response reflected by increases in oxygen-containing surface functional groups of biochar, including C-O-C (51.35 % - 149 %) and N-C-O (65.55 % - 119 %). Pearson correlation and RDA analysis indicated that the chemical properties of biochar contribute more to the carbon-source utilization properties of biochar colonized microbial community within 1 month of incubation, while the bulk soil chemical properties (pH, DOC, MBC and NO

Although biochar is considered a promising C sequestration agent, long-term field experiments are lacking to assess the effects of biochar addition on the soil organic C (SOC) and microbial community. Corn ( L.) straw feedstock and biochar were applied to a sandy loam soil for three consecutive years to investigate the SOC distribution within various fractionations, responses of soil microbial biomass, enzyme activity, and community structure. In comparison with straw amendment, higher levels of biochar (6.0 and 12 t ha) significantly increased soil pH, SOC, total N (TN), available P (AP) and available K. Biochar (12 t ha) decreased the fulvic acid fraction by 15.9% and increased the free-light C (FLC), intra-aggregate, and organomineral fractionations by 6.05-, 2.52-, and 0.22-fold, respectively. There was no significant influence of straw or biochar application on the soil microbial biomass C (MBC) contents or the activities of soil enzymes. A phospholipid fatty acids assay suggested that 6.0 t ha straw slightly enriched the abundance of Actinobacteria in soil, whereas biochar (6.0 and 12 t ha) mainly promoted the growth of Gram-positive bacteria, fungi, and general bacteria groups. Canonical correspondence analysis indicated that soil pH, SOC, TN, AP, FLC, and fulvic acid significantly influence the structure of soil microbial community (-0.50,0.05 for both MBC and the ratio of MBC to SOC;0.50 for microbial biomass N, basal respiration [BR], and the ratio of BR through incubation to MBC). Established quantitative relationships provided evidence for understanding the effects of biochar amendment on soil environment after a long-term field application.

Many previous research have investigated the spatial distribution of the content of soil organic matter (SOM) and soil humic substance (HS), while few work focused on the chemical composition variation of HS across geographic distance. Paddy soils, collected from different long-term fertilization treatments across a wide geographic area in subtropical China, were used to evaluate the spatial variation of HS chemical composition. The 3-dimensional fluorescence spectroscopy combined with parallel factor analysis was used to evaluate the chemical composition of the soil extractable humic substance (EHS, including humic acid and fulvic acid). Analysis of distance-decay relationship (DDR) was introduced here to study the spatial variation of the chemical compositions of these EHSs. It was found that geographic location impose greater impact on the compositional variation of soil EHS than fertilization practice. Fertilization treatments including NPK (mineral N, P and K fertilizers) and NPKS (NPK fertilizers plus straw return) exhibited significant flattened DDR slopes as compared to CK (no fertilizers), which indicated fertilization (NPK and NPKS) decreased the variation of EHS chemical composition in paddy soils across geographic distance. A positive correlation was found between variations of soil bacterial community and EHS chemical composition, and fertilization (NPK and NPKS) enhanced their relationships. This work demonstrated that although the geographic location mainly dominated the spatial variation of the soil EHS chemical composition across geographic distance, the same long-term fertilization practice could gradually domesticate the paddy soils to display more similar EHS composition.

Recent works have shown that long-term fertilization has a critical influence on soil microbial communities; however, the underlying ecological assemblage of microbial community as well as its linkage with soil fertility and crop yield are still poorly understood. In this study, using analysis of high-throughput sequencing of 16S rRNA gene amplicons, we investigate mean pairwise phylogenetic distance (MPD), nearest relative index (NRI), taxonomic compositions and network topological properties to evaluate the assembly of the soil microbial community developed in 30-year fertilized soils. The phylogenetic signal indicates that environmental filtering was a more important assembly process that structure the microbial community than the stochastic process. Increase of soil fertility indexes, such as cation exchange capacity (CEC), soil organic matter (SOM) and available P (AP), driven by balanced fertilizations and straw returning amendment, result in the decrease of environmental filtering on the bacterial community assembly. Network parameters show that the amendment of straw returning provides with more niches, which lead to more complex phylotype co-occurrence. Increase of crop yield under balanced fertilizations might due to the increase of soil microbial function traits, which is associated with decreasing influence of environmental filtering. The significantly increased bacterial genera, Candidatus Koribacter, Candidatus Solibacter, and Fimbriimonas, in straw returning treatments, might be the key species in the competition caused by long-term environmental filtering. These results are helpful for a unified understanding of the ecological processes for microbial communities in different fertilized agroecosystem and the development of sustainable agriculture.

To determine bacterial communities involved, directly or indirectly, in the anaerobic degradation of cellulose, we conducted a microcosm experiment with soil treated with 13C-cellulose, 12C-cellulose, or without cellulose with analyses of DNA-based stable isotope probing (DNA-SIP), real-time quantitative PCR, and high-throughput sequencing. Firmicutes, Actinobacteria, Verrucomicrobia, and Fibrobacteres were the dominant bacterial phyla-degrading cellulose. Generally, bacteria possessing gene-encoding enzymes involved in the degradation of cellulose and hemicellulose were stimulated. Phylotypes affiliated to Geobacter were also stimulated by cellulose, probably due to their role in electron transfer. Nitrogen-fixing bacteria were also detected, probably due to the decreased N availability during cellulose degradation. High-throughput sequencing showed the presence of bacteria not incorporating 13C and probably involved in the priming effect caused by the addition of cellulose to soil. Collectively, our findings revealed that a more diverse microbial community than expected directly and indirectly participated in anaerobic cellulose degradation.

Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM-in response to nutrient addition-influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.

Microbial communities, coupled with substrate quality and availability, regulate the stock (formation versus mineralization) of soil organic matter (SOM) in terrestrial ecosystems. However, our understanding of how soil microbes interact with contrasting substrates influencing SOM quantity and quality is still very superficial. Here, we used thermodynamic theory principles and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the linkages between dissolved organic matter (DOM [organic substrates in soil that are readily available]), thermodynamic quality, and microbial communities. We investigated soils from subtropical paddy ecosystems across a 1,000-km gradient and comprising contrasting levels of SOM content and nutrient availability. Our region-scale study suggested that soils with a larger abundance of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and higher SOM content. We further advocated a novel phylotype-level microbial classification based on their associations with OM quantities and qualities and identified two contrasting clusters of bacterial taxa: phylotypes that are highly positively correlated with thermodynamically favorable DOM and larger SOM content versus those which are associated with less-favorable DOM and lower SOM content. Both groups are expected to play critical roles in regulating SOM contents in the soil. By identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities and should be considered in models of soil organic matter preservation.IMPORTANCE Microbial communities are known to be important drivers of organic matter (OM) accumulation in terrestrial ecosystems. However, despite the importance of these soil microbes and processes, the mechanisms behind these microbial-SOM associations remain poorly understood. Here, we used the principles of thermodynamic theory and novel Fourier transform ion cyclotron resonance mass spectrometry techniques to investigate the links between microbial communities and dissolved OM (DOM) thermodynamic quality in soils across a 1,000-km gradient and comprising contrasting nutrient and C contents. Our region-scale study provided evidence that soils with a larger amount of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and larger SOM content. Moreover, we created a novel phylotype-level microbial classification based on the associations between microbial taxa and DOM quantities and qualities. We found two contrasting clusters of bacterial taxa based on their level of association with thermodynamically favorable DOM and SOM content. Our study advances our knowledge on the important links between microbial communities and SOM. Moreover, by identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities. Together, our findings support that the association between microbial species taxa and substrate thermodynamic quality constituted an important complement explanation for soil organic matter preservation.

Background The soil disease-suppressiveness may depend on complex interactions between pathogens and microbiome in response to limiting nutrients. However, these interactions remain poorly understood. Thus, we investigated the significance of soil available phosphorus (AP) in modulating pathogen-microbiome interactions for the emergence or suppression of peanut wilt using receiver operating characteristic curve (ROC) analysis and structural equation modeling (SEM) approaches. Results We observed significant differences in the relative abundance of pathogenic and beneficial microbes, alpha- and beta-diversity indices between disease-conducive and -suppressive soils. The pathogenic ( Ralstonia) and beneficial ( Burkholderia and Bacillus ) taxa dominated the rhizosphere of wilted and healthy peanut plants. The rhizosphere of healthy rather than wilted plants showed significantly higher microbial biodiversity. Moreover, co-occurrences between Ralstonia and microbiome species were highly positive and negative in the disease-conducive and -suppressive soil, respectively, thus predicting facilitative ( Rudaea ) and suppressive ( Burkholderia , Enterobacter , Bacillus ) role of indigenous microbes in Ralstonia invasion in soil. Moreover, both ROC and SEM analyses revealed that Ralstonia invaded rhizospheric microbial networks and caused peanut wilt, very likely by competently utilizing soil phosphorus under copiotrophic (high AP) than oligotrophic (low AP) conditions. Conclusion Our results suggest the importance of soil phosphorus availability in altering the interactions between pathobiome and beneficial microbiome. Our study concludes that feeding soil with labile nutrients could deplete microbial biodiversity and interactions while paving the way for pathogen invasion.

The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.

Elucidation of the inhibitory effects of humic substances (HSs) on phytopathogenic fungi and the underlying molecular mechanisms are highly important for improved biocontrol. In this study, we investigated the growth suppression, morphological characteristics, transcriptomic sequence, and radical signals of Rhizoctonia solani following HS addition (50 mg/L). Through mycelial cultured experiment, mycelia growth of R. solani had been suppressed with HS addition, and the inhibition rate was 24.88 ± 0.11% compared to the control. Field emission-scanning electron microscopy showed increased and superimposed branching mycelial growth, with a shriveled appearance. RNA samples of R. solani cultured with or without HSs were both extracted to examine the sequence on molecular level by Illumina HiSeq sequencing platform. RNA sequencing analysis revealed 175 differentially expressed genes (DEGs; 111 upregulated and 64 downregulated) between the HSs treatment and control. The upregulated unigenes were annotated and significantly enriched to three molecular processes: vitamin B6 metabolism, ABC transporters, and glutathione metabolism, while the downregulated unigenes were annotated to carbohydrate metabolism, but not significantly enriched. Real time-quantitative polymerase chain reaction analysis showed that the unigenes related to hexokinase, glucose-6-phosphate isomerase, glutathione synthase, and glutathione reductase were significantly decreased (by 60.03%, 70.70%, 60.33%, and 57.59%, respectively), while those related to glutathione S-transferase were significantly increased (2.66-fold). The electron paramagnetic resonance spectra showed that HSs induced increased the intensity of radical signals of R. solani in a cultured system increased by 59.56% compared to CK (without HSs addition). Network analysis based on DEGs expression and the chemical structure of HSs revealed that the carbonyl moiety in HSs formed the most links with nodes of the DEGs (sum of the links of positive and negative effects = 70), implicating this structure as the active fraction responsible for the inhibitory effect. This study provides molecular and chemical evidence of the biofungicidal activity of HSs with the potential for practical application.

The overuse of antibiotics and subsequent enrichment of antibiotic resistant microbes in the natural and built environments is a severe threat to global public health. In this study, a Phanerochaete chrysosporium fungal-luffa fiber system was found to efficiently biodegrade two sulfonamides, sulfadimethoxine (SDM) and sulfadizine (SDZ), in cow urine wastewater. Biodegradation pathways were proposed on the basis of key metabolites identified using high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (HPLC-QqTOF-MS). Transcriptomic, metabolomic, and free radical analyses were performed to explore the functional groups and detailed molecular mechanisms of SDM and SDZ degradation. A total of 27 UniGene clusters showed significant differences between luffa fiber and luffa fiber-free systems, which were significantly correlated to cellulose catabolism, carbohydrate metabolism, and oxidoreductase activity. Carbohydrate-active enzymes and oxidoreductases appear to play particularly important roles in SDM and SDZ degradation. Electron paramagnetic resonance (EPR) spectroscopy revealed the generation and evolution of OH and R during the biodegradation of SDM and SDZ, suggesting that beyond enzymatic degradation, SDM and SDZ were also transformed through a free radical pathway. Luffa fiber also acts as a co-substrate to improve the activity of enzymes for the degradation of SDM and SDZ. This research provides a potential strategy for removing SDM and SDZ from agricultural and industrial wastewater using fungal-luffa fiber systems.

To select optimal fertilization management for soil productivity and fertilizer-nitrogen use efficiency (NUE) improvement in rice fields, we conducted a microplot experiment by growing rice in soils from different long-term fertilizations with the same inorganic fertilizers. The NUE was accurately evaluated using 15N labeled urea. The variations of the chemical compositions of soil organic carbon (SOC) under different long-term fertilizations were investigated by three-dimensional fluorescence measurement. The results indicated that the treatments containing organic materials could maintain high soil productivities and displayed higher NUE than inorganic treatments. Total phosphorus (TP) was the most important soil factor for soil productivity and the SOC content ranked second, whereas SOC content was the primary soil factor affecting NUE and TP ranked second. Applying organic materials also significantly changed the chemical compositions of SOC as compared with inorganic treatments. Besides the SOC content, the chemical compositions of SOC also affect the soil productivity and NUE. In summary, long-term balanced application of inorganic fertilizers and organic materials increased the quantity and changed the chemical composition of SOC, and thus maintained high soil productivity and NUE.

Dissolved organic matter (DOM) and microbial biomass (MB) are small but reactive pools of soil organic matter (SOM). The incorporation of carbon (C) from rice residue into DOM and MB in paddy soils under aerobic condition when rice straw remains in the field is poorly understood. A one-year incubation experiment was conducted, in which 13C-labelled rice straw was added to a cultivation chronosequence of paddy soils ranging from 0 to 100 years. Rice straw was rapidly decomposed during the first 30 days, after which 73% of the added straw C, on average, was retained in the soil and 46% of the straw C remained in the soil after one year. Throughout the entire incubation period, 0.2–0.9% of the added straw C was incorporated into DOM, and 2–5% was recovered in MB. The paddy cultivation age strongly affected the straw contribution to the organic C pools. In barren land (0 year), 32–60% of the DOM was derived from straw C, while 13–30% of the DOM was derived from straw C in 5–100-year paddy soils. On average, straw C contributed to 88% of the MB in barren land, 50% in 5-year soil, and 13% in 100-year soil. Consequently, over the duration of paddy cultivation, the contribution of rice straw C to the MB decreased, while the contribution of SOM increased. Our study has indicated that DOM in paddy soils mainly originates from SOM rather than from added plant residues but that plant residues are an important C source for microorganisms.

Long-term intensive cultivation and heavy fertilization improve the nutritional conditions in acidic Ultisols, but also sharply accelerate soil acidification. However, the impact of such dramatic environmental changes on soil microorganisms is unclear. The aims of this work were to investigate the responses of microbial community composition and metabolic function to long-term fertilization, and to determine the key factors that primarily drive microbial changes in acidic Ultisols. A long-term fertilization experiment under a winter wheat–summer maize rotation was established in 1990 in acidic Ultisols of southern China. Soils were collected from four treatments in June 2014: (1) non-fertilization control (CK); (2) only N fertilization (N); (3) N, P, and K fertilization (NPK); and (4) NPK plus manure (NPKM; 70% of total N obtained from manure). The amount of N used in all N treatments was 300 kg N ha−1 year−1. The soil pH, cation exchange capacity (CEC), soil organic carbon (SOC), total nitrogen (TN), phosphorus (TP) and potassium (TK), available nitrogen (AN), phosphorus (AP), and potassium (AK) were measured. Soil microbial community composition and metabolic function were determined by phospholipid fatty acids analysis (PLFA) and community-level physiological profile (CLPP) method, respectively. Compared with CK, NPKM significantly increased total PLFA biomass and average well color development (AWCD); NPK increased total PLFA biomass by 2.2 times, but its AWCD was not significantly different from CK, indicating that microbial metabolic efficiency in NPK decreased. N decreased total PLFA biomass by 27.9%, while almost completely inhibiting metabolic activity. NPKM maintained microbial functional diversity indexes at similar levels as CK, while NPK and N significantly decreased microbial functional diversity indexes. Redundancy analysis (RDA) revealed that soil microbial community composition and metabolic pattern were more stably maintained by application of manure compared to chemical fertilizers. Soil pH showed the primary effect on microbial community composition, metabolic activity, and functional diversity indexes. This research demonstrated that the negative effects of Ultisol acidification induced by long-term application of chemical N fertilizer on microorganisms overwhelmed the positive effects of soil nutrition improvement. The inhibiting effect of serious acidification on microbial metabolic function was stronger than that on community composition. Microorganisms live in a low active metabolic state to resist serious Ultisols acidification. Therefore, fertilization in acidic Ultisols should be based on the premise of preventing soil further acidification.

Understanding the soil dissolved organic matter (DOM) chemodiversity and its interaction with microbes is crucial to comprehend the biogeochemical processes in soil. In this study, ultrahigh-resolution fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) was employed to in detail characterize the DOM chemodiversity at a molecular level. The variation of the DOM chemodiversity from four agro-ecological experimental sites (paddy fields) subjected to different long-term fertilizations across different distance-points was evaluated. Geographic distance had a greater impact on DOM chemodiversity than anthropogenic fertilization. Distance-decay analysis showed that the dissimilarity of the DOM chemodiversity significantly increased with the increase in geographic distance. Long-term organic fertilizations homogenized the DOM chemodiversity as it made lipid-like compounds more similar regardless of geography. A network analysis combining DOM chemodiversity and bacterial community composition showed the significant interactions between bacteria species and DOM molecules. Variable partitioning analysis (VPA) showed that the bacterial community diversity dictates the soil DOM chemodiversity and not vice versa. Geographic distance indirectly affects the soil DOM chemodiversity by shaping the bacterial community.

Abundant phosphorus (P) has been applied to paddy fields in the red soil region of subtropical China. Microbial communities play important roles in soil nutrient cycling; however, the effects of P surplus on soil microbial diversity and community composition are still unclear. Soils collected from paddy fields in subtropical China was incubated and subjected to four P treatments: 33 kg ha−1 (CK), 66 kg ha−1 (P1), 132 kg ha−1 (P2), and 264 kg ha−1 (P3). Changes in bacterial and fungal diversity and community composition were evaluated by high-throughput sequencing. The different P rates had no significant effect on bacterial diversity, whereas fungal richness and diversity indexes declined significantly by increasing P rates. Principle coordinate analysis (PCoA) also indicated a shift in fungal community composition when P rates were higher than 132 kg ha−1. Available P (AP) was the dominant factor affecting fungal community composition as evaluated by canonical correspondence analysis (CCA). Multivariate regression trees (MRT) revealed that the key threshold of 53.6 mg kg−1 of AP divided treatments into two distinct groups. Linear discriminant analysis effect size (LEfSe) showed that abundances of Pseudogymnoascus and Geomyces increased, but those of Penicillium and an unknown genus of Trichocomaceae decreased when AP was ≥ 53.6 mg kg−1.