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Abstract Background The conversion of plant biomass into biochemicals is a promising way to alleviate energy shortage, which depends on efficient microbial saccharification and cellular metabolism. Trichoderma spp. have plentiful CAZymes systems that can utilize all-components of lignocellulose. Acetylation of polysaccharides causes nanostructure densification and hydrophobicity enhancement, which is an obstacle for glycoside hydrolases to hydrolyze glycosidic bonds. The improvement of deacetylation ability can effectively release the potential for polysaccharide degradation. Results Ammonium sulfate addition facilitated the deacetylation of xylan by inducing the up-regulation of multiple carbohydrate esterases (CE3/CE4/CE15/CE16) of Trichoderma harzianum. Mainly, the pathway of ammonium-sulfate's cellular assimilates inducing up-regulation of the deacetylase gene (Thce3) was revealed. The intracellular metabolite changes were revealed through metabonomic analysis. Whole genome bisulfite sequencing identified a novel differentially methylated region (DMR) that existed in the ThgsfR2 promoter, and the DMR was closely related to lignocellulolytic response. ThGsfR2 was identified as a negative regulatory factor of Thce3, and methylation in ThgsfR2 promoter released the expression of Thce3. The up-regulation of CEs facilitated the substrate deacetylation. Conclusion Ammonium sulfate increased the polysaccharide deacetylation capacity by inducing the up-regulation of multiple carbohydrate esterases of T. harzianum, which removed the spatial barrier of the glycosidic bond and improved hydrophilicity, and ultimately increased the accessibility of glycosidic bond to glycoside hydrolases.

Summary: The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.

ABSTRACT Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.IMPORTANCERalstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.

Abstract In several filamentous fungi, incident light and environmental stress signaling share the mitogen‐activated protein kinase (MAPK) HOG (SAK) pathway. It has been revealed that short‐term illumination with blue light triggers the activation of the HOG pathway in Trichoderma spp. In this study, we demonstrate the crucial role of the basic leucine zipper transcription factor ATF1 in blue light responses and signaling downstream of the MAPK HOG1 in Trichoderma guizhouense. The lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial germination. Upon blue light or H2O2 stimuli, HOG1 interacted with ATF1 in the nucleus. Genome‐wide transcriptome analyses revealed that 61.8% (509 out of 824) and 85.2% (702 out of 824) of blue light‐regulated genes depended on ATF1 and HOG1, respectively, of which 58.4% (481 out of 824) were regulated by both of them. Our results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the dark. Additionally, the lack of ATF1 led to reduced oxidative stress resistance, probably because of the downregulation of catalase‐encoding genes. Overall, our results demonstrate that ATF1 is the downstream component of HOG1 and is responsible for blue light responses, conidial germination, vegetative growth, and oxidative stress resistance in T. guizhouense.

ABSTRACT Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

ABSTRACT The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.IMPORTANCEThe assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Gibberella stalk rot (GSR) caused by the fungus Fusarium graminearum is a devastating disease of maize (Zea mays L.), but we lack efficient methods to control this disease. Biological control agents, including beneficial microorganisms, can be used as an effective and eco-friendly approach to manage crop diseases. For example, Bacillus velezensis SQR9, a bacterial strain isolated from the rhizosphere of cucumber plants, promotes growth and suppresses diseases in several plant species. However, it is not known whether and how SQR9 affects maize resistance to GSR. In this study, we found that treatment with SQR9 increased maize resistance to GSR by activating maize induced systemic resistance (ISR). RNA-seq and quantitative reverse transcription-PCR analysis showed that phenylpropanoid biosynthesis, amino acid metabolism, and plant-pathogen interaction pathways were enriched in the root upon colonization by SQR9. Also, several genes associated with calcium signaling pathways were up-regulated by SQR9 treatment. However, the calcium signaling inhibitor LaCl3 weakened the SQR9-activated ISR. Our data suggest that the calcium signaling pathway contributes to maize GSR resistance via the activation of ISR induced by SQR9. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

ABSTRACT Microbes typically reside in communities containing multiple species, whose interactions have considerable impacts on the robustness and functionality of such communities. To manage microbial communities, it is essential to understand the factors driving their assemblage and maintenance. Even though the community composition could be easily assessed, interspecies interactions during community establishment remain poorly understood. Here, we combined co-occurrence network analysis with quantitative PCR to examine the importance of each species within synthetic communities (SynComs) of pellicle biofilms. Genome-scale metabolic models and in vitro experiments indicated that the biomass of SynComs was primarily affected by keystone species that are acting either as metabolic facilitators or as competitors. Our study sets an example of how to construct a SynCom and investigate interspecies interactions.IMPORTANCECo-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.

Abstract Bacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For B. amyloliquefaciens, B. pumilus, and B. megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that the gyrA gene may have broad application prospects in the study of Bacillus ecology.

ABSTRACT Seed-associated microbiomes can impact the later colonization of a plant rhizosphere microbiome. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome may intervene in the assembly of a rhizosphere microbiome. In this study, the fungus Trichoderma guizhouense NJAU4742 was introduced to both maize and watermelon seed microbiomes by seed coating. Application was found to significantly promote seed germination and improve plant growth and rhizosphere soil quality. The activities of acid phosphatase, cellulase, peroxidase, sucrase, and α-glucosidase increased significantly in two crops. The introduction of Trichoderma guizhouense NJAU4742 also led to a decrease in the occurrence of disease. Coating with T. guizhouense NJAU4742 did not alter the alpha diversities of the bacterial and fungal communities but formed a key network module that contained both Trichoderma and Mortierella. This key network module comprised of these potentially beneficial microorganisms was positively linked with the belowground biomass and activities of rhizosphere soil enzymes but negatively correlated with disease incidence. Overall, this study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome. IMPORTANCE Seed-associated microbiomes can impact the rhizosphere microbiome assembly and function display. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome with the beneficial microbes may intervene in the assembly of a rhizosphere microbiome. Here, we introduced T. guizhouense NJAU4742 to the seed microbiome by seed coating. This introduction led to a decrease in the occurrence of disease and an increase in plant growth; furthermore, it formed a key network module that contained both Trichoderma and Mortierella. Our study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome.

Abstract Background Filamentous fungi are highly efficient at deconstructing plant biomass by secreting a variety of enzymes, but the complex enzymatic regulation underlying this process is not conserved and remains unclear. Results In this study, cellulases and xylanases could specifically respond to Avicel- and xylan-induction, respectively, in lignocellulose-degrading strain Trichoderma guizhouense NJAU4742, however, the differentially regulated cellulases and xylanases were both under the absolute control of the same TgXyr1-mediated pathway. Further analysis showed that Avicel could specifically induce cellulase expression, which supported the existence of an unknown specific regulator of cellulases in strain NJAU4742. The xylanase secretion is very complex, GH10 endoxylanases could only be induced by Avicel, while, other major xylanases were significantly induced by both Avicel and xylan. For GH10 xylanases, an unknown specific regulator was also deduced to exist. Meanwhile, the post-transcriptional inhibition was subsequently suggested to stop the Avicel-induced xylanases secretion, which explained the specifically high xylanase activities when induced by xylan in strain NJAU4742. Additionally, an economical strategy used by strain NJAU4742 was proposed to sense the environmental lignocellulose under the carbon starvation condition, that only slightly activating 4 lignocellulose-degrading genes before largely secreting all 33 TgXyr1-controlled lignocellulases if confirming the existence of lignocellulose components. Conclusions This study, aiming to explore the unknown mechanisms of plant biomass-degrading enzymes regulation through the combined omics analysis, will open directions for in-depth understanding the complex carbon utilization in filamentous fungi.

Probiotic Bacillus colonization of plant root surfaces has been reported to improve its beneficial effect. Chemotaxis, adhesion, aggregation, and biofilm formation are the four steps of root colonization by plant growth–promoting rhizobacteria (PGPRs). Compared with the other three well-studied processes, adhesion of PGPRs is less known. In this study, using mutant strains deleted for potential adhesin genes in PGPR strain Bacillus velezensis SQR9, adherence to both cucumber root surface and abiotic surface by those strains was evaluated. Results showed that deletion mutations ΔlytB, ΔV529_10500, ΔfliD, ΔyhaN, and ΔsacB reduced the adhesion to root surfaces, while, among them, only ΔfliD had significant defects in adhesion to abiotic surfaces (glass and polystyrene). In addition, B. velevzensis SQR9 mutants defective in adhesion to root surfaces showed a deficiency in rhizosphere colonization. Among the encoded proteins, FliD and YhaN played vital roles in root adhesion. This research systematically explored the potential adhesins in a well-studied PGPR strain and also indicated that adhesion progress was required for root colonization, which will help to enhance rhizosphere colonization and beneficial function of PGPRs in agricultural production.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract Severe early defoliation has become an important factor restricting the development of the pear industry in southern China. However, the assembly patterns of microbial communities and their functional activities in response to the application of bioorganic fertilizer (BIO) or humic acid (HA) in southern China’s pear orchards remain poorly understood, particularly the impact on the early defoliation of the trees. We conducted a 3-year field experiment (2017–2019) in an 18-year-old ‘Cuiguan’ pear orchard. Four fertilization schemes were tested: local custom fertilization as control (CK), CK plus HA (CK-HA), BIO, and BIO plus HA (BIO-HA). Results showed that BIO and BIO-HA application decreased the early defoliation rate by 50–60%, and increased pear yield by 40% compared with the CK and CK-HA treatments. The BIO and BIO-HA application significantly improved soil pH, available nutrient content, total enzyme activity and ecosystem multifunctionality, and also changed the structure of soil bacterial and fungal communities. The genus Acidothermus was positively correlated with the early defoliation rate, while the genus Rhodanobacter was negatively correlated. Additionally, random forest models revealed that the early defoliation rate could be best explained by soil pH, ammonium content, available phosphorus, and total enzyme activity. In conclusion, application of BIO or BIO mixed with HA could have assembled distinct microbial communities and increased total enzyme activity, leading to significant improvement of soil physicochemical traits. The increased availability of soil nutrient thus changed leaf nutrient concentrations and alleviated the early defoliation rate of pear trees in acid red soil in southern China.

ABSTRACT Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.

ABSTRACT Kin discrimination in nature is an effective way for bacteria to stabilize population cooperation and maintain progeny benefits. However, so far, the research on kin discrimination for Bacillus still has concentrated on “attack and defense” between cells and diffusion-dependent molecular signals of quorum sensing, kin recognition in Bacillus, however, has not been reported. To determine whether flagellar is involve in the kin recognition of Bacillus, we constructed Bacillus velezensis SQR9 assembled with flagellin of its kin and non-kin strains, and performed a swarm boundary assay with SQR9, then analyzed sequence variation of flagellin and other flagellar structural proteins in B. velezensis genus. Our results showed that SQR9 assembled with flagellin of non-kin strains was more likely to form a border phenotype with wild-type strain SQR9 in swarm assay than that of kin strains, and that non-kin strains had greater variation in flagellin than kin strains. In B. velezensis, these variations in flagellin were prevalent and had evolved significantly faster than other flagellar structural proteins. Therefore, we proposed that flagellin is an effective tool partly involved in the kin recognition of B. velezensis strains. IMPORTANCE Kin selection plays an important role in stabilizing population cooperation and maintaining the progeny benefits for bacteria in nature. However, to date, the role of flagellin in kin recognition in Bacillus has not been reported. By using rhizospheric Bacillus velezensis SQR9, we accomplished flagellin region interchange among its related strains, and show that flagellin acts as a mediator to distinguish kin from non-kin in B. velezensis. We demonstrated the polymorphism of flagellin in B. velezensis through alignment analysis of flagellin protein sequences. Therefore, it was proposed that flagellin was likely to be an effective tool for mediating kin recognition in B. velezensis.

ABSTRACT Global climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates. IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.

Trichoderma is a genus of filamentous fungi that play notable roles in stimulating plant growth after colonizing the root surface. However, the key proteins and molecular mechanisms governing this stimulation have not been completely elucidated. In this study, Trichoderma guizhouense NJAU 4742 was investigated in a hydroponic culture system after interacting with cucumber roots. The total proteins of the fungus were characterized, and the key metabolic pathways along with related genes were analyzed through proteomic and transcriptomic analyses. The roles played by the regulated proteins during the interaction between plants and NJAU 4742 were further examined. The intracellular or extracellular proteins from NJAU 4742 and extracellular proteins from cucumber were quantified, and the high-abundance proteins were determined which were primarily involved in the shikimate pathway (tryptophan, tyrosine, and phenylalanine metabolism, auxin biosynthesis, and secondary metabolite synthesis). Moreover, 15N-KNO3 labeling analysis indicated that NJAU 4742 had a strong ability to convert nitrogenous amino acids, nitrate, nitrile, and amines into ammonia. The auxin synthesis and ammonification metabolism pathways of NJAU 4742 significantly contributed to plant growth. The results of this study demonstrated the crucial metabolic pathways involved in the interactions between Trichoderma spp. and plants.

Abstract Fusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.

Microorganisms are the most abundant and diverse organisms in soils and have important effects on soil fertility. In this study, effects of the long-term fertilization treatments no fertilizer (CK), chemical fertilizer (nitrogen–phosphorus–potassium (NPK)), and organic–inorganic fertilizer (NPK and organic fertilizer (NPKM)) on rice yield and soil bacterial and fungal community diversity, structure, composition, and interaction networks were evaluated. Of the three treatments, the highest rice yield was in NPKM. Bacterial richness was significantly higher in NPKM than in NPK. Fertilization treatment significantly altered β diversity of communities, species composition of bacterial and fungal communities, and structure of soil microbial networks. The most complex bacterial and fungal interaction co-occurrence network with the highest average degree and numbers of edges and nodes was in NPKM. Relative abundance of the plant growth-promoting fungus Trichoderma increased significantly in NPKM compared with CK and NPK. The results of the study indicate that bacterial richness and microbial community member interactions (network complexity) might be suitable indicators of soil biological fertility. This research provides new insights on the effects of different fertilization regimes on responses of soil bacterial and fungal communities and their contributions to crop yield. New indicators such as bacterial richness and complexity of microbial interaction networks are also identified that can be used to evaluate soil biological fertility.

ABSTRACT Plant rhizobiomes consist of microbes that are influenced by the physical, chemical, and biological properties of the plant root system. While plant-microbe interactions are generally thought to be local, accumulating evidence suggests that topologically disconnected bulk soil microbiomes could be linked with plants and their associated rhizospheric microbes through volatile organic compounds (VOCs). While several studies have focused on the effect of soil physicochemical properties for VOC movement, it is less clear how VOC signaling is affected by microbial communities themselves when VOCs travel across soils. To gain a better understanding of this, we propose that soil microbe-plant communities could be viewed as “metarhizobiomes,” where VOC-mediated interactions extend the plant rhizobiome further out through interconnected microbial metapopulation networks. In this minireview, we mainly focus on soil microbial communities and first discuss how microbial interactions within a local population affect VOC signaling, leading to changes in the amount, type, and ecological roles of produced VOCs. We then consider how VOCs could connect spatially separated microbial populations into a larger metapopulation network and synthesize how (i) VOC effects cascade in soil matrix when moving away from the source of origin and (ii) how microbial metapopulation composition and diversity shape VOC-signaling between plants and microbes at the landscape level. Finally, we propose new avenues for experimentally testing VOC movement in plant-microbe metapopulation networks and suggest how VOCs could potentially be used for managing plant health in natural and agricultural soils.

Abstract Survival of inoculated fungal strains in a new environment plays a critical role in functional performance, but few studies have focused on strain-specific quantitative PCR (qPCR) methods for monitoring beneficial fungi. In this study, the Trichoderma guizhouense strain NJAU 4742 (transformed with the gfp gene and named gfp-NJAU 4742), which exhibits a growth-promoting effect by means of phytohormone production and pathogen antagonism, was selected as a model to design strain-specific primer pairs using two steps of genomic sequence comparison to detect its abundance in soil. After a second comparison with the closely related species T. harzianum CBS 226-95 to further differentiate the strain-specific fragments that had shown no homology to any sequence deposited in the databases used in the first comparison, ten primer pairs were designed from the whole genome. Meanwhile, 3 primer pairs, P11, P12 and P13, were also designed from the inserted fragment containing the gfp gene. After verification testing with three types of field soils, primer pairs P6, P7 and P8 were further selected by comparison with P11, P12 and P13. A practical test using a pot experiment showed that stable colonization of gfp-NJAU 4742 in pepper rhizosphere soil could be detected using primer pairs P6 and P7, showing no significant difference from the results of primers P11 and P12. Hence, the strategy described here for designing fungal-strain-specific primers may theoretically be used for any other fungi for which the whole genome sequence is available in a database, and the qPCR methodology developed can also be used to further monitor the population dynamics of different strains based on the designed primers.

Abstract Background Colonization of Trichoderma spp. is essential for exerting their beneficial functions on the plant. However, the interactions between Trichoderma spp. and plant roots are still not completely understood. The aim of this study was to investigate how TgSWO affect Trichoderma guizhouense to establish themselves in the plant rhizosphere and promote plant growth. In this study, we deeply analyzed the molecular mechanism by which the functional characterization of the TgSWO by expressing different functional region deletion proteins (FRDP) of TgSWO. Results Root scanning analysis results showed that TgSWO could dramatically increase root density and promote growth. In addition, we also found that TgSWO could expand root cell walls, subsequently increase root colonization. Moreover, knockout of TgSWO mutants (KO) or overexpression of TgSWO mutants (OE) produced greatly reduced or increased the number of cucumber root, respectively. To clarify the molecular mechanism of TgSWO in plant-growth-promotion, we analyzed the ability of different FRDP to expand the root cell wall. The root cell wall architecture were considerably altered when treated by ΔCBD protein (the TgSWO gene of lacking in the CBD domain was cloned and heterologously expressed), in correlation with the present YoaJ domain of TgSWO. In contrast, neither the expansion of cell walls nor the increase of roots was detectable in ΔYoaJ protein. Conclusions Our results emphasize the YoaJ domain is the most critical functional area of TgSWO during the alteration of cell wall architecture. Simultaneously, the results obtained in this study also indicate that TgSWO might play a plant-growth-promotion role in the Trichoderma-plant interactions by targeting the root cell wall.

Composting is an environmentally friendly way to turn plant and animal wastes into organic fertilizers. However, it is unclear to what extent the source of animal waste products (such as manure) affects the physicochemical and microbiological properties of compost. Here, we experimentally tested how the type of livestock manure of herbivores (sheep and cattle) and omnivores (pig and chicken) influences the bacterial and fungal communities and physicochemical properties of compost. Higher pH, NO3-N, Total carbon (TC) content and C/N were found in sheep and cattle manure composts, while higher EC, NH4-N, Total nitrogen (TN) and total phosphorus (TP) content were measured in pig and chicken manure composts. Paired clustering between herbivore and omnivore manure compost metataxonomy composition was also observed at both initial and final phases of composting. Despite this clear clustering, all communities changed drastically during the composting leading to reduced bacterial and fungal diversity and large shifts in community composition and species dominance. While Proteobacteria and Chloroflexi were the major phyla in sheep and cattle manure composts, Firmicutes dominated in pig and chicken manure composts. Together, our results indicate that feeding habits of livestock can determine the biochemical and biological properties of manures, having predictable effects on microbial community composition and assembly during composting. Manure metataxonomy profiles could thus potentially be used to steer and manage composting processes.

ABSTRACT Fertilization regimes are known to drive succession of the soil microbial community, whereas the assembly rules involved remain elusive. Moreover, the ecological roles of microbial “generalists” and “specialists” in soils with contrasting fertilization regimes have not been characterized. We explored how long-term fertilization regimes (i.e., treatments conducted for at least 30 years) impact the soil bacteria by modifying species richness, diversity, bacterial assembly, and niche breadth. Compared with long-term organic fertilizer input, the soils having undergone chemical-only fertilization contained smaller amounts of carbon resources and had a more acidic environment. This strong environmental constraint lowered the soil bacterial reservoir and resulted in a detectable ecoevolutionary transformation, with both a higher proportion of specialists and a stronger signature of deterministic processes. Overall, this study provided a new comprehensive understanding of the assembly rules of bacterial generalists and specialists under long-term fertilization regimes. This study also highlighted that chemical-only fertilization, a ubiquitous agricultural practice of current conventional agriculture, induced a strong and similar environmental force that transformed the soil microbiota from 28°N to 46°N included in this study. IMPORTANCE Chemical-only fertilization is ubiquitous in contemporary conventional agriculture despite the fact that sustainability of this agricultural practice is increasingly being questioned because of the current observed soil degradation. We explored how long-term chemical-only versus organic-only fertilizations impacted the soil microbiota reservoir in terms of both diversity and induced assembly processes. The results showed that long-term chemical-only fertilization resulted in deep selection pressure on the soil microbial community reservoir, with both a higher proportion of specialists and a stronger signature of deterministic processes. The soil microbiota has clearly changed as a consequence of the fertilization regime. The diagnoses of the functional consequences of these ecoevolutionary changes in relation to agricultural practices are key to imagining agriculture in the time ahead and especially regarding future efforts for the conservation, restoration, and management of the soil microbiota reservoir which is key to the fertility of the ecosystem.

ABSTRACT Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secreted siderophore molecules might influence microbial interaction outcomes. Here, we tested if bacterial interactions mediated by iron-scavenging siderophores can be used to predict the disease suppressiveness of microbial consortia against soilborne Ralstonia solanacearum, a bacterial pathogen in the tomato rhizosphere. Iron availability significantly affected the interactions within inoculated consortia and between the consortia and the pathogen. We observed contrasting effects of siderophores and other nonsiderophore metabolites on the pathogen growth, while the siderophore effects were relatively much stronger. Specifically, disease incidence was reduced in vivo when the inoculated consortia produced siderophores that the pathogen could not use for its own growth. Employing siderophore-mediated interactions to engineer functionally robust microbial inoculants shows promise in protecting plants from soilborne pathogens. IMPORTANCE Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens.

ABSTRACT Maintaining stability of ecosystem functions in the face of global change calls for a better understanding regulatory factors of functionally specialized microbial groups and their population response to disturbance. In this study, we explored this issue by collecting soils from 54 managed ecosystems in China and conducting a microcosm experiment to link disturbance, elemental stoichiometry, and genetic resistance. Soil carbon:nitrogen:phosphorus (C:N:P) stoichiometry imparted a greater effect on the abundance of microbial groups associated with main C, N, and P biogeochemical processes in comparison with mean annual temperature and precipitation. Nitrogen cycling genes, including bacterial amoA-b, nirS, narG, and norB, exhibited the highest genetic resistance to N deposition. The amoA-a and nosZ genes exhibited the highest resistance to warming and drying-wetting cycles, respectively. Soil total C, N, and P contents and their ratios had a strong direct effect on the genetic resistance of microbial groups, which was dependent on mean annual temperature and precipitation. Specifically, soil C/P ratio was the main predictor of N cycling genetic resistance to N deposition. Soil total C and N contents and their ratios were the main predictors of P cycling genetic resistance to N deposition, warming, and drying-wetting. Overall, our work highlights the importance of soil stoichiometric balance for maintaining the ability of ecosystem functions to withstand global change. IMPORTANCE To be effective in predicting future stability of soil functions in the context of various external disturbances, it is necessary to follow the effects of global change on functionally specialized microbes related to C and nutrient cycling. Our study represents an exploratory effort to couple the stoichiometric drivers to microbial populations related with main C, N, and P cycling and their resistances to global change. The abundance of microbial groups involved in cellulose, starch, and xylan degradation, nitrification, N fixation, denitrification, organic P mineralization, and inorganic P dissolution showed a high stoichiometry dependency. Resistance of these microbial populations to global change could be predicted by soil C:N:P stoichiometry. Our work highlights that stoichiometric balance in soil C and nutrients is instrumental in maintaining the stability and adaptability of ecosystem functions under global change.

Abstract Xylanase with a high thermostability will satisfy the needs of raising the temperature of hydrolysis to improve the rheology of the broth in industry of biomass conversion. In this study, a xylanase gene (xyn10A), predicted to encode a hydrolase domain of GH10, a linker region and a CBM1 domain, was cloned from a superior lignocellulose degrading strain Aspergillus fumigatus Z5 and successfully expressed in Pichia pastoris X33. Xyn10A has a specific xylanase activity of 34.4 U mg−1, and is optimally active at 90 °C and pH 6.0. Xyn10A shows quite stable at pHs ranging from 3.0 to 11.0, and keeps over 40% of xylanase activity after incubation at 70 °C for 1 h. Removal of CBM1 domain has a slight negative effect on its thermostability, but the further cleavage of linker region significantly decreased its stability at high temperature. The transfer of CBM1 and linker region to another GH10 xylanase can help to increase the thermostability. In addition, hydrolase domains between the two Xyn10A proteins naturally formed a dimer structure, which became more thermostable after removing the CBM1 or/and linker region. This thermostable Xyn10A is a suitable candidate for the highly efficient fungal enzyme cocktails for biomass conversion.

Abstract Paenibacillus polymyxa (SQR-21) is not only a plant growth-promoting rhizobacteria, but also an effective biocontrol agent against Fusarium wilt disease of watermelon. For the better understanding and clarifying the potential mechanisms of SQR-21 to improve watermelon growth and disease resistance, a split-root methodology in hydroponic and LC–MS technology with the label free method was used to analyze the key root proteins involved in watermelon metabolism and disease resistance after the inoculation of SQR-21. Out of 623 identified proteins, 119 proteins were differentially expressed when treatment (SQR-21 inoculation) and control (no bacterial inoculation) were compared. Among those, 57 and 62 proteins were up-regulated and down-regulated, respectively. These differentially expressed proteins were identified to be involved in signal transduction (ADP-ribosylation factor, phospholipase D), transport (aspartate amino-transferase), carbohydratemetabolic (glucose-6-phosphate dehydrogenase, UDP-glucose pyrophosphorylase), defense and response to stress (glutathione S-transferase, Ubiquitin-activating enzyme E1), and oxidation–reduction process (thioredoxin peroxidase, ascorbate peroxidase). The results of this study indicated that SQR-21 inoculation on the watermelon roots benefits plant by inducing the expression of several proteins involved in growth, photosynthesis, and other metabolic and physiological activities.

The inoculation of plants with plant-growth-promoting rhizobacterium has been an effective strategy for enhancing plant salt tolerance to diminish the loss of agricultural productivity caused by salt stress; however, the signal transmitted from bacteria to the plant under salt stress is poorly understood. In this study, the salt tolerance of Arabidopsis thaliana and Zea mays was enhanced by inoculation with Bacillus amyloliquefaciens SQR9. Using dialysis bags with different molecular weight cutoffs, we sorted through the molecules secreted by SQR9 and found that spermidine is responsible for enhancing plant salt tolerance. An SQR9 ΔspeB mutant deficient in spermidine production failed to induce plant salt tolerance. However, the induction of plant salt tolerance was disrupted by mutating genes involved in reduced glutathione (GSH) biosynthesis and the salt overly sensitive pathway in Arabidopsis. Using quantitative real-time polymerase chain reaction, this study demonstrated that spermidine produced by SQR9 leads to increased glutamine synthetase and glutathione reductase gene expression, leading to increased levels of GSH, which is critical for scavenging reactive oxygen species. SQR9-derived spermidine also upregulates the expression of NHX1 and NHX7, which sequesters Na+ into vacuoles and expels Na+ from the cell, thereby reducing ion toxicity.

Colonization of plant growth–promoting rhizobacteria (PGPR) is critical for exerting their beneficial effects on the plant. Root exudation is a major factor influencing the colonization of both PGPR and soil-borne pathogens within the root system. However, the tripartite interaction of PGPR, plant roots, and soil-borne pathogens is poorly understood. We screened root exudates for signals that mediate tripartite interactions in the rhizosphere. In a split-root system, we found that root colonization of PGPR strain Bacillus amyloliquefaciens SQR9 on cucumber root was significantly enhanced by preinoculation with SQR9 or the soil-borne pathogen Fusarium oxysporum f. sp. cucumerinum, whereas root colonization of F. oxysporum f. sp. cucumerinum was reduced upon preinoculation with SQR9 or F. oxysporum f. sp. cucumerinum. Root exudates from cucumbers preinoculated with SQR9 or F. oxysporum f. sp. cucumerinum were analyzed and 109 compounds were identified. Correlation analysis highlighted eight compounds that significantly correlated with root colonization of SQR9 or F. oxysporum f. sp. cucumerinum. After performing colonization experiments with these chemicals, raffinose and tryptophan were shown to positively affect the root colonization of F. oxysporum f. sp. cucumerinum and SQR9, respectively. These results indicate that cucumber roots colonized by F. oxysporum f. sp. cucumerinum or SQR9 increase root secretion of tryptophan to strengthen further colonization of SQR9. In contrast, these colonized cucumber roots reduce raffinose secretion to inhibit root colonization of F. oxysporum f. sp. cucumerinum.

Soil-borne diseases, especially those caused by fungal pathogens, lead to profound annual yield losses. One key example for such a disease is Fusarium wilt disease in banana. In some soils, plants do not show disease symptoms, even if the disease-causing pathogens are present. However, the underlying agents that make soils suppressive against Fusarium wilt remain elusive. In this study, we aimed to determine the underlying microbial agents governing soil disease-suppressiveness. We traced the shift of microbiomes during the invasion of disease-causing Fusarium oxysporum f. sp. cubense in disease-suppressive and disease-conducive soils. We found distinct microbiome structures in the suppressive and conducive soils after pathogen invasion. The alpha diversity indices increased (or did not significantly change) and decreased, respectively, in the suppressive and conducive soils, indicating that the shift pattern of the microbiome with pathogen invasion was notably different between the suppressive and conductive soils. Microbiome networks were more complex with higher numbers of links and revealed more negative links, especially between bacterial taxa and the disease-causing Fusarium, in suppressive soils than in conducive soils. We identified the bacterial genera Chryseolinea, Terrimonas, and Ohtaekwangia as key groups that likely confer suppressiveness against disease-causing Fusarium. Overall, our study provides the first insights into agents potentially underlying the disease suppressiveness of soils against Fusarium wilt pathogen invasion. The results of this study may help to guide efforts for targeted cultivation and application of these potential biocontrol agents, which might lead to the development of effective biocontrol agents against Fusarium wilt disease.

Mechanisms by which beneficial rhizobacteria promote plant growth include tryptophan-dependent indole-3-acetic acid (IAA) synthesis. The abundance of tryptophan in the rhizosphere, however, may influence the level of benefit provided by IAA-producing rhizobacteria. This study examined the cucumber-Bacillus amyloliquefaciens SQR9 system and found that SQR9, a bacterium previously shown to enhance the growth of cucumber, increased root secretion of tryptophan by three- to fourfold. Using a split-root system, SQR9 colonization of roots in one chamber not only increased tryptophan secretion from the noninoculated roots but also increased the expression of the cucumber tryptophan transport gene but not the anthranilate synthesis gene in those roots. The increased tryptophan in isolated rhizosphere exudates was sufficient to support increased IAA production by SQR9. Moreover, SQR9 colonization of roots in one chamber in the split-root system resulted in sufficient tryptophan production by the other roots to upregulate SQR9 IAA biosynthesis genes, including a 27-fold increase in the indole-3-acetonitrilase gene yhcX during subsequent colonization of those roots. Deletion of yhcX eliminated SQR9-mediated increases in root surface area, likely by reducing IAA-stimulated lateral root growth. This study demonstrates a chemical dialogue between B. amyloliquefaciens and cucumber in which this communication contributes to bacteria-mediated plant-growth enhancement.

Banana production is seriously hindered by Meloidogyne spp. all over the world. Endophytes are ideal candidates compared to pesticides as an environmentally benign agent. In the present study, endophytes isolated from banana roots infected by Meloidogyne spp. with different disease levels were tested in vitro, and in sterile and nature banana monoculture soils against Meloidogyne javanica. The proportion of antagonistic endophytes were higher in the roots of middle and high disease levels. Among those, bacteria were dominant, and Pseudomonas spp., Bacillus spp. and Streptomyces spp. showed more abundant populations. One strain, named as SA, with definite root inner-colonization ability was isolated and identified as Streptomyces sp. This strain showed an inhibiting rate of >50% in vitro and biocontrol efficiency of 70.7% in sterile soil against Meloidogyne javanica, compared to the control. Greenhouse experiment results showed that the strain SA exhibits excellent biological control ability for plant-parasites both in roots and in root-knot nematode infested soil. SA treatment showed a higher number of bacterivores, especially Mesorhabditis and Cephalobus. The maturity index was significantly lower, while enrichment index (EI) was significantly higher in the SA treatment. In conclusion, this study presents an important potential application of the endophytic strain Streptomyces sp. for the control of plant-parasitic nematodes, especially Meloidogyne javanica, and presents the effects on the associated variation of the nematode community.

The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analysed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three OTUs belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community composition were correlated with organic matter composition in maize rhizosphere soil and the application of manure could activate more AMF species to interact with other species in the maize rhizosphere. This knowledge can be valuable in regulating the symbiotic system of plants and AMF, maintaining the health and high yields of crops and providing a primary basis for rational fertilization.

Macrolactin produced by many soil microbes has been shown to be an efficient antibacterial agent against many bacterial pathogens. However, studies examining the effect of macrolactin on both the soil bacterial community and the intrinsic bacterial species that harbor genes responsible for the production of this antibiotic have not been conducted so far. In this study, a mixture of macrolactin was isolated from the liquid culture of Bacillus amyloliquefaciens NJN-6, and applied to the soil once a week for four weeks. 16S rRNA Illumina MiSeq sequencing showed that continuous application of macrolactin reduced the α-diversity of the soil bacterial community and thereby changed the relative abundance of microbes at both the phylum and genus level. The relative abundance of Proteobacteria and Firmicutes was significantly increased along with a significant decrease in the relative abundance of Acidobacteria. However, the application of macrolactins had an insignificant effect on the total numbers of bacteria. Further, the native gene responsible for the production of macrolactin, the gene encoding polyketide synthase (PKS) was reduced in copy number after the application of macrolactin. The results of this study suggested that a bactericide from a microbial source could decrease the diversity of the soil bacterial community and change the bacterial community structure. Moreover, the populations of the intrinsic bacterial species which harbor genes responsible for macrolactin production were inhibited when the external source antibiotic was applied.

Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilizer (OF). Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with organic fertilizer application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR versus sequence analysis, yet poor correlations were found for the Alpha- and Beta- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.

High-quality bio-organic fertilizers (BIOs) cannot be produced without the addition of some proteins. In this study, compound liquid amino acids (CLAA) from animal carcasses were utilized as additives into matured composts to create novel BIOs containing plant growth-promoting rhizobacteria (PGPR). The results showed that adding CLAA and inoculating bacteria meanwhile resulted in failed solid-state fermentation (SSF) due to the higher H+ contents. While after pre-compost for 4 days before PGPR inoculation, treatments of matured chicken or pig manure added with 0.2 ml g-1 of CLAA resulted in a maximum biomass of functional strains. Illumine-MiSeq sequencing and Real-Time PCR results showed that the CLAA addition decreased the bacterial abundance and richness, altered the bacterial community structure and changed the relative abundance of some microbial groups. This study offers a high value-added utilization of waste protein resources for producing economical, high-quality BIO.