Bacillus velezensis SQR9 promotes plant growth through colonization and rhizosphere-phyllosphere bacteria interaction.

The rhizosphere and phyllosphere of plants are home to a diverse range of microorganisms that play pivotal roles in ecosystem services. Consequently, plant growth-promoting bacteria (PGPB) are extensively utilized as inoculants to enhance plant growth and boost productivity. Despite this, the interactions between the rhizosphere and phyllosphere, which are influenced by PGPB inoculation, have not been thoroughly studied to date. In this study, we inoculated Bacillus velezensis SQR9, a PGPB, into the bulk soil, rhizosphere or phyllosphere, and subsequently examined the bacterial communities in the rhizosphere and phyllosphere using amplicon sequencing. Our results revealed that PGPB inoculation increased its abundance in the corresponding compartment, and all treatments demonstrated plant growth promotion effects. Further analysis of the sequencing data indicated that the presence of PGPB exerted a more significant impact on bacterial communities in both the rhizosphere and phyllosphere than in the inoculation compartment. Notably, the PGPB stimulated similar rhizosphere-beneficial microbes regardless of the inoculation site. We, therefore, conclude that PGPB can promote plant growth both directly and indirectly through the interaction between the rhizosphere and phyllosphere, leading to the enrichment of beneficial microorganisms.

Predatory protists reduce bacteria wilt disease incidence in tomato plants.

Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.

Moderately delayed maturation of composting promotes the reduction of guild-plant pathogenic fungi within vegetable waste.

The relationships among the relative abundance of guild-plant pathogenic fungi, compost maturation index, and microbial community variation during vegetable waste composting, which are influenced by the C/N ratio, remain poorly understood. To address this, fungal communities were analyzed in composting treatments with C/N ratios of approximately 15 (CN15) and 25 (CN25), using vegetable waste as the primary raw material. The CN15 treatment showed greater microbial community variation and a better overall compost maturation index value than the CN25 treatment. However, the CN25 treatment had a greater decline in plant-pathogenic fungi than the CN15 treatment. Notably, the relative abundance of guild-plant pathogenic fungi was significantly negatively related to the compost maturity index in the CN25 treatment, while no significant relationship was observed in the CN15 treatment. This study suggests that the moderately delayed maturation of composting is beneficial for reducing guild-plant pathogenic fungi in vegetable waste.

Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production.

The soil microbiota is critical to plant performance. Improving the ability of plant-associated soil probiotics is thus essential for establishing dependable and sustainable crop yields. Although fertilizer applications may provide an effective way of steering soil microbes, it is still unknown how the positive effects of soil-borne probiotics can be maximized and how their effects are mediated. This work aims to seek the ecological mechanisms involved in cabbage growth using bio-organic fertilizers. We conducted a long-term field experiment in which we amended soil with non-sterilized organic or sterilized organic fertilizer either containing Trichoderma guizhouense NJAU4742 or lacking this inoculum and tracked cabbage plant growth and the soil fungal community. Trichoderma-amended bio-organic fertilizers significantly increased cabbage plant biomass and this effect was attributed to changes in the resident fungal community composition, including an increase in the relative abundance and number of indigenous soil growth-promoting fungal taxa. We specifically highlight the fundamental role of the biodiversity and population density of these plant-beneficial fungal taxa in improving plant growth. Together, our results suggest that the beneficial effects of bio-organic fertilizer seem to be a combination of the biological inoculum within the organic amendment as well as the indirect promotion through effects on the diversity and composition of the soil resident plant-beneficial fungal microbiome.

Rhizosphere Microbiota Promotes the Growth of Soybeans in a Saline-Alkali Environment under Plastic Film Mulching.

The rhizosphere microbiota plays a critical and crucial role in plant health and growth, assisting plants in resisting adverse stresses, including soil salinity. Plastic film mulching is an important method to adjust soil properties and improve crop yield, especially in saline-alkali soil. However, it remains unclear whether and to what extent the association between these improvements and rhizosphere microbiota exists. Here, from a field survey and a greenhouse mesocosm experiment, we found that mulching plastic films on saline-alkali soil can promote the growth of soybeans in the field. Results of the greenhouse experiment showed that soybeans grew better in unsterilized saline-alkali soil than in sterilized saline-alkali soil under plastic film mulching. By detecting the variations in soil properties and analyzing the high-throughput sequencing data, we found that with the effect of film mulching, soil moisture content was effectively maintained, soil salinity was obviously reduced, and rhizosphere bacterial and fungal communities were significantly changed. Ulteriorly, correlation analysis methods were applied. The optimization of soil properties ameliorated the survival conditions of soil microbes and promoted the increase in relative abundance of potential beneficial microorganisms, contributing to the growth of soybeans. Furthermore, the classification of potential key rhizosphere microbial OTUs were identified. In summary, our study suggests the important influence of soil properties as drivers on the alteration of rhizosphere microbial communities and indicates the important role of rhizosphere microbiota in promoting plant performance in saline-alkali soil under plastic film mulching.

Plant pathogen resistance is mediated by recruitment of specific rhizosphere fungi.

Beneficial interactions between plants and rhizosphere microorganisms are key determinants of plant health with the potential to enhance the sustainability of agricultural practices. However, pinpointing the mechanisms that determine plant disease protection is often difficult due to the complexity of microbial and plant-microbe interactions and their links with the plant's own defense systems. Here, we found that the resistance level of different banana varieties was correlated with the plant's ability to stimulate specific fungal taxa in the rhizosphere that are able to inhibit the Foc TR4 pathogen. These fungal taxa included members of the genera Trichoderma and Penicillium, and their growth was stimulated by plant exudates such as shikimic acid, D-(-)-ribofuranose, and propylene glycol. Furthermore, amending soils with these metabolites enhanced the resistance of a susceptible variety to Foc TR4, with no effect observed for the resistant variety. In total, our findings suggest that the ability to recruit pathogen-suppressive fungal taxa may be an important component in determining the level of pathogen resistance exhibited by plant varieties. This perspective opens up new avenues for improving plant health, in which both plant and associated microbial properties are considered.

Root-Associated Antagonistic Pseudomonas spp. Contribute to Soil Suppressiveness against Banana Fusarium Wilt Disease of Banana.

Members of the microbiotas colonizing the plant endophytic compartments and the surrounding bulk and rhizosphere soil play an important role in determining plant health. However, the relative contributions of the soil and endophytic microbiomes and their mechanistic roles in achieving disease suppression remain elusive. To disentangle the relative importance of the different microbiomes in the various plant compartments in inhibiting pathogen infection, we conducted a field experiment to track changes in the composition of microbial communities in bulk and rhizosphere soil and of root endophytes and leaf endosphere collected from bananas planted on Fusarium-infested orchards in disease-suppressive and disease-conducive soils. We found that the rhizosphere and roots were the two dominant plant parts whose bacterial communities contributed to pathogen suppression. We further observed that Pseudomonas was potentially a key organism acting as a pathogen antagonist, as illustrated by microbial community composition and network analysis. Subsequently, culturable pathogen-antagonistic Pseudomonas strains were isolated, and their potential suppressive functions or possible antibiosis in terms of auxin or siderophore synthesis and phosphate solubilization were screened to analyze the mode of action of candidate disease-suppressive Pseudomonas strains. In a follow-up in vivo and greenhouse experiment, we revealed that microbial consortia of culturable Pseudomonas strains P8 and S25 (or S36), isolated from banana plantlet rhizosphere and roots, respectively, significantly suppressed the survival of pathogens in the soil, manipulated the soil microbiome, and stimulated indigenous beneficial microbes. Overall, our study demonstrated that root-associated microbiomes, especially the antagonistic Pseudomonas sp. components, contribute markedly to soil suppression of banana Fusarium wilt. IMPORTANCE Soil suppression of Fusarium wilt disease has been proven to be linked with the local microbial community. However, the contribution of endophytic microbes to disease suppression in wilt-suppressive soils remains unclear. Moreover, the key microbes involving in Fusarium wilt-suppressive soils and in the endophytic populations have not been fully characterized. In this study, we demonstrate that root-associated microbes play vitally important roles in disease suppression. Root-associated Pseudomonas consortia were recognized as a key component in inhibiting pathogen abundance associated with the host banana plants. This finding is crucial to developing alternate strategies for soilborne disease management by harnessing the plant microbiome.

Additive fungal interactions drive biocontrol of Fusarium wilt disease.

Host-associated fungi can help protect plants from pathogens, and empirical evidence suggests that such microorganisms can be manipulated by introducing probiotic to increase disease suppression. However, we still generally lack the mechanistic knowledge of what determines the success of probiotic application, hampering the development of reliable disease suppression strategies. We conducted a three-season consecutive microcosm experiment in which we amended banana Fusarium wilt disease-conducive soil with Trichoderma-amended biofertilizer or lacking this inoculum. High-throughput sequencing was complemented with cultivation-based methods to follow changes in fungal microbiome and explore potential links with plant health. Trichoderma application increased banana biomass by decreasing disease incidence by up to 72%, and this effect was attributed to changes in fungal microbiome, including the reduction in Fusarium oxysporum density and enrichment of pathogen-suppressing fungi (Humicola). These changes were accompanied by an expansion in microbial carbon resource utilization potential, features that contribute to disease suppression. We further demonstrated the disease suppression actions of Trichoderma-Humicola consortia, and results suggest niche overlap with pathogen and induction of plant systemic resistance may be mechanisms driving the observed biocontrol effects. Together, we demonstrate that fungal inoculants can modify the composition and functioning of the resident soil fungal microbiome to suppress soilborne disease.

Organic fertilization enhances the resistance and resilience of soil microbial communities under extreme drought.

INTRODUCTION: The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought. OBJECTIVES: This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers. METHODS: In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes. RESULTS: Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting. CONCLUSION: Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning.

Partitioning the Effects of Soil Legacy and Pathogen Exposure Determining Soil Suppressiveness via Induced Systemic Resistance.

Beneficial host-associated bacteria can assist plant protection against pathogens. In particular, specific microbes are able to induce plant systemic resistance. However, it remains largely elusive which specific microbial taxa and functions trigger plant immune responses associated with disease suppression. Here, we experimentally studied this by setting up two independent microcosm experiments that differed in the time at which plants were exposed to the pathogen and the soil legacy (i.e., soils with historically suppressive or conducive). Overall, we found soil legacy effects to have a major influence on disease suppression irrespective of the time prior to pathogen exposure. Rhizosphere bacterial communities of tomato plants were significantly different between the two soils, with potential beneficial strains occurring at higher relative abundances in the suppressive soil. Root transcriptome analysis revealed the soil legacy to induce differences in gene expression, most importantly, genes involved in the pathway of phenylpropanoid biosynthesis. Last, we found genes in the phenylpropanoid biosynthesis pathway to correlate with specific microbial taxa, including Gp6, Actinomarinicola, Niastella, Phaeodactylibacter, Longimicrobium, Bythopirellula, Brevundimonas, Ferruginivarius, Kushneria, Methylomarinovum, Pseudolabrys, Sphingobium, Sphingomonas, and Alterococcus. Taken together, our study points to the potential regulation of plant systemic resistance by specific microbial taxa, and the importance of soil legacy on disease incidence and eliciting plant-defense mechanisms.

Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt.

Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.

Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application.

The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.

Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances.

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.

Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health.

Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However, little is known regarding the impact of microbiome predators on plant health-influencing microbes and the interactive links to plant health. Here, we aimed to decipher the importance of predator-prey interactions in influencing plant health. To achieve this goal, we investigated soil and root-associated microbiomes (bacteria, fungi and protists) over nine years of banana planting under conventional and organic fertilization regimes differing in Fusarium wilt disease incidence. We found that the reduced disease incidence and improved yield associated with organic fertilization could be best explained by higher abundances of protists and pathogen-suppressive bacteria (e.g. Bacillus spp.). The pathogen-suppressive actions of predatory protists and Bacillus spp. were mainly determined by their interactions that increased the relative abundance of secondary metabolite Q genes (e.g. nonribosomal peptide synthetase gene) within the microbiome. In a subsequent microcosm assay, we tested the interactions between predatory protists and pathogen-suppressive Bacillus spp. that showed strong improvements in plant defense. Our study shows how protistan predators stimulate disease-suppressive bacteria in the plant microbiome, ultimately enhancing plant health and yield. Thus, we suggest a new biological model useful for improving sustainable agricultural practices that is based on complex interactions between different domains of life.

Patterns of fungal community succession triggered by C/N ratios during composting.

Accumulating evidence indicates that the functional rather than taxonomic composition of microbial communities is closely correlated to local environmental factors. While composting is a widely accepted practice, specific knowledge of how fungal functional groups interact during the composting process remains limited. To address this, the impact of the initial C/N ratio of composting material on fungal community was analyzed in order to reveal the succession of functional diversity. Compared with the raw materials, the final composting product significantly reduced the relative abundances of plant and animal pathogens. Abundances of plant and animal pathogens, as well as dung saprotrophs, were negatively correlated with compost maturity, while abundances of wood saprotrophs exhibited positive correlations. Specific OTUs that showing highly abundant in each treatment were expected to compete for environmental preferences (niches) and/or interact with each other in positive (facilitative) ways. OTU2 (wood saprotroph) exhibiting the highest occurrence was negatively related to OTU7 (animal pathogen) and OTU4 (plant pathogen) during the mesophilic phase. Taken together, high-efficiency composting is represented as pattern variations of fungal community with a process of gradual decline of plant and animal pathogens as well as dung saprotrophs.

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression.

BACKGROUND: Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. RESULTS: To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. CONCLUSION: Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function. Video Abstract.

Heat stress during late gestation disrupts maternal microbial transmission with altered offspring's gut microbial colonization and serum metabolites in a pig model.

Heat stress (HS) during gestation has been associated with negative outcomes, such as preterm birth or postnatal metabolic syndromes. The intestinal microbiota is a unique ecosystem playing an essential role in mediating the metabolism and health of mammals. Here we hypothesize late gestational HS alters maternal microbial transmission and structures offspring's intestinal microbiota and serum metabolic profiles. Our results show maternal HS alters bacterial ß-diversity and composition in sows and their piglets. In the maternal intestine, genera Ruminococcaceae UCG-005, [Eubacterium] coprostanoligenes group and Halomonas are higher by HS (q < 0.05), whereas the populations of Streptococcus, Bacteroidales RF16 group_norank and Roseburia are decreased (q < 0.05). In the maternal vagina, HS mainly elevates the proportions of phylum Bacteroidetes and Fusobacteria (q < 0.05), whereas reduces the population of Clostridiales Family XI (q < 0.05). In the neonatal intestine, maternal HS promotes the population of Proteobacteria but reduces the relative abundance of Firmicutes (q < 0.05). Moreover, the core Operational taxonomic units (OTU) analysis indicates the proportions of Clostridium sensu stricto 1, Romboutsia and Turicibacter are decreased by maternal HS in the intestinal and vaginal co-transmission, whereas that of phylum Proteobacteria and Epsilonbacteraeota, such as Escherichia-Shigella, Klebsiella, Acinetobacter, and Comamonas are increased in both the intestinal and vaginal co-transmission and the vagina. Additionally, Aeromonas is the only genus that is transmitted from environmental sources. Lastly, we evaluate the importance of neonatal differential OTU for the differential serum metabolites. The results indicate Acinetobacter significantly contributes to the differences in the adrenocorticotropic hormone (ACTH) and glucose levels due to HS (P < 0.05). Further, Stenotrophomonas is the most important variable for Cholesterol, low-density lipoprotein (LDL), diamine oxidase (DAO), blood urea nitrogen (BUN) and 5-hydroxytryptamine (5-HT) (P < 0.10). Overall, our data provides evidence for the maternal HS in establishing the neonatal microbiota via affecting maternal transmission, which in turn affects the maintenance of metabolic health.

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Taking banana continuous planting soil with high banana fusarium wilt disease incidence as a test site, we examined the effect of lime and ammonium carbonate fumigation coupled with bio-organic fertilizer on the suppression of banana fusarium wilt disease and the structure and composition of bacterial community, using real-time quantitative PCR and high-throughput sequencing. The results showed that the disease incidence was reduced by 13.3% and 21.7% in the treatments of LAOF (lime and ammonium carbonate fumigation coupled with organic fertilizer) and LABF (lime and ammonium carbonate fumigation coupled with bio-organic fertilizer), respectively, compared with OF (application of organic fertilizer without fumigation), while the copy number of Fusarium was decreased by 22.4% and 33.0%, respectively. Compared with non-fumigation treatment, lime and ammonium fumigation coupled with different fertilizer applications significantly reduced bacteria richness and diversity, with different community structure, while fumigation had a decisive effect on bacterial community composition. Bacterial richness and diversity of LABF were lower than those of other treatments, while microbial community structure was clearly disparate from other treatments. Compared with non-fumigation treatment, the relative abundance of Mizugakiibacter, Brucella, and Rhodanobacter were significantly improved in the fumigation coupled with different fertilization treatments. Those three genera in LABF were higher than those in LAOF, with significant differences for the relative abundances of Mizugakiibacter and Brucella. Therefore, fumigation combined with bio-organic fertilizer application could reduce the copy number of pathogen, alter soil bacterial community structure and stimulate beneficial bacteria in the resident soil, and thus reduce the occurrence of banana fusarium wilt.

Lime and ammonium carbonate fumigation coupled with bio-organic fertilizer application steered banana rhizosphere to assemble a unique microbiome against Panama disease.

Microbiome plays a key role in determining soil suppressiveness against invading pathogens. Our previous study revealed that microbial community of bulk soil could be manipulated by lime and ammonium bicarbonate fumigation followed by biofertilizer application. However, the assembly of microbial community suppressive to banana Panama disease in the rhizosphere is still unclear. In this study, we used high-throughput sequencing and quantitative PCR to explore the assembly of rhizosphere microbiome associated with banana Panama disease suppression in a two-seasonal pot experiment. We found biofertilizer applied to lime and ammonium bicarbonate fumigated soil significantly (P < 0.05) reduced the abundance of rhizosphere Fusarium oxysporum compared to biofertilizer applied to non-fumigated soil. Principal coordinate analysis revealed that biofertilizer applied to lime and ammonium bicarbonate fumigated soil re-shaped the rhizosphere bacterial community composition by increasing the phylogenetic relatedness, and stimulating indigenous microbes, for example, Gemmatimonas, Sphingomonas, Pseudomonas, Lysobacter and Bacillus. Co-occurrence analysis revealed that potential species involved in disease suppression were more interrelated in disease-suppressive soils. Taken together, lime and ammonium bicarbonate fumigation followed by biofertilizer application could induce banana rhizosphere to assemble beneficial microbes dominated consortia to suppress banana Panama disease.

Isolation of Antagonistic Endophytes from Banana Roots against Meloidogyne javanica and Their Effects on Soil Nematode Community.

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.