Deep 16S rRNA pyrosequencing reveals a bacterial community associated with Banana Fusarium Wilt disease suppression induced by bio-organic fertilizer application

Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants

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.

The occurrence of clubroot in cruciferous crops correlates with the chemical and microbial characteristics of soils

Clubroot disease, caused by Plasmodiophora brassicae, is a serious soil-borne disease in Brassica crops worldwide. It seriously occurs in conducive soils of southern China, while never happens in some areas of northern China with suppressive soils. To understanding the differences, we measured the soil suppressiveness, chemical properties, and microbial communities in suppressive and conducive soils by bioassay and sequencing of 16S and 18S rRNA amplicons. The biological basis of clubroot suppressiveness was supported by the ability to remove it by pasteurization. The pH value and calcium content in the suppressive soils were higher than those in the conducive soils. Suppressive soils were associated with higher fungal diversity and bacterial abundance. The fungal phyla Chytridiomycota, Olpidiomycota, and Mucoromycota and the bacterial phyla Acidobacteriota and Gemmatimonadota were enriched in suppressive soils. More abundant beneficial microbes, including Chaetomium and Lysobacter, were found in the suppressive soils than in the conducive soils. Molecular ecological network analysis revealed that the fungal network of suppressive soils was more complex than that of conducive soils. Our results indicate that plant health is closely related to soil physicochemical and biological properties. This study is of great significance for developing strategies for clubtroot disease prevention and control.

Identification of the gut microbiota affecting Salmonella pullorum and their relationship with reproductive performance in hens

Introduction

Pullorum disease is one of the common bacterial infectious diseases caused by Salmonella pullorum (S. pullorum), which can result in a decrease in the reproductive performance of laying hens, thus causing considerable economic losses. However, studies about the characteristics of intestinal microbiota with pullorum and their potential association with reproductive performance in hens are still limited. This study was to identify the gut microbiota associated with S. pullorum in poultry.

Methods

A total of 30 hens with S. pullorum-negative (PN) and 30 hens with S. pullorum-positive (PP) were analyzed for hatching eggs laid in 2 weeks (HEL), fertilization eggs (FE), chick number (CN), and microbial structure.

Results

There were significant differences in HEL (p < 0.01), FE (p < 0.01), and CN (p < 0.01) between PP and PN. Histomorphological observations showed abnormal morphology of the ovaries and fallopian tubes and low integrity of epithelial tissue in the ileum and cecum in PP. 16S rRNA gene sequencing revealed that beneficial cecal microbes, such as Bacteroides, Desulfovibrio, and Megamonas, were positively correlated with reproductive performance and had lower abundance in PP (p = 0.001). Furthermore, diminished phosphotransferase system (PTS) and pentose phosphate pathway, butanoate metabolism and oxidative phosphorylation were also found in PP.

Discussion

Taken together, this study clarified the morphological characteristics of the reproductive tract and intestines of chickens infected with S. pullorum and preliminarily explored the potential association between cecal microbiota and reproductive performance in hens. Our data may provide a reference for revealing the intestinal microbial characteristics of hens in resisting pullorum and exploring novel approaches to infection control in future studies.

Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil

One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information needs to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH^• ) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system, and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a 'cry for help' case, wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.

Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem

BACKGROUND

Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta.

RESULTS

We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages.

CONCLUSIONS

Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Root exudates increased arsenic mobility and altered microbial community in paddy soils

Root exudates are crucial for plants returning organic matter to soils, which is assumed to be a major source of carbon for the soil microbial community. This study investigated the influence of root exudates on the fate of arsenic (As) with a lab simulation experiment. Our findings suggested that root exudates had a dose effect on the soil physicochemical properties, As speciation transformation and the microbial community structure at different concentrations. The addition of root exudates increased the soil pH while decreased the soil redox potential (Eh). These changes in the soil pH and Eh increased As and ferrous (Fe(II)) concentrations in soil porewater. Results showed that 40 mg/L exudates addition significantly increased arsenite (As(III)) and arsenate (As(V)) by 541 and 10 times respectively within 30 days in soil porewater. The relative abundance of Fe(III)-reducing bacteria Geobacter and Anaeromyxobacter increased with the addition of root exudates, which enhanced microbial Fe reduction. Together these results suggest that investigating how root exudates affect the mobility and transformation of As in paddy soils is helpful to systematically understand the biogeochemical cycle of As in soil-rice system, which is of great significance for reducing the health risk of soil As contamination.

Effect of incorporation of broccoli residues into soil on occurrence of verticillium wilt of spring-sowing-cotton and on rhizosphere microbial communities structure and function

Cotton verticillium wilt (CVW) represented a typical plant soil-borne disease and resulted in widespread economic losses in cotton production. However, the effect of broccoli residues (BR) on verticillium wilt of spring-sowing-cotton was not clear. We investigated the effects of BR on CVW, microbial communities structure and function in rhizosphere of two cotton cultivars with different CVW resistance using amplicon sequencing methods. Results showed that control effects of BR on CVW of susceptible cultivar (cv. EJ-1) and resistant cultivar (cv. J863) were 58.49% and 85.96%, and the populations of V. dahliae decreased by 14.31% and 34.19%, respectively. The bacterial diversity indices significantly increased in BR treatment, while fungal diversity indices significantly decreased. In terms of microbial community composition, the abilities to recruit bacteria and fungi were enhanced in BR treatment, including RB41, Gemmatimonas, Pontibacter, Streptomyces, Blastococcus, Massilia, Bacillus, and Gibberella, Plectosphaerella, Neocosmospora, Aspergillus and Preussia. However, the relative abundances of Sphingomonas, Nocardioides, Haliangium, Lysobacter, Penicillium, Mortierella and Chaetomidium were opposite tendency between cultivars in BR treatment. According to PICRUSt analysis, functional profiles prediction showed that significant shifts in metabolic functions impacting KEGG pathways of BR treatment were related to metabolism and biosynthesis. FUNGuild analysis indicated that BR treatment altered the relative abundances of fungal trophic modes. The results of this study demonstrated that BR treatment decreased the populations of V. dahliae in soil, increased bacterial diversity, decreased fungal diversity, changed the microbial community structure and function, and increased the abundances of beneficial microorganisms.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Identification of Gut Microbiota Affecting Fiber Digestibility in Pigs

Dietary fiber plays an important role in porcine gut health and welfare. Fiber is degraded by microbial fermentation in the intestine, and most gut microbiota related to fiber digestibility in pigs are worth pursuing. The aim of this study was to identify gut microbiota associated with the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF) and of acid detergent fiber (ADF) in pigs. Large phenotypic variations in the ATTD of NDF and of ADF were separately found among 274 Suhuai pigs. Microbial community structures were significantly different between high and low fiber digestibility groups. Fourteen genera separately dominated the communities found in the high ATTD (H-AD) of NDF and ADF samples and were in very low abundance in the low ATTD (L-AD) of NDF and ADF samples. In conclusion, norank_f__Bacteroidales_S24-7_group (p < 0.05), Ruminococcaceae_UCG-005 (p < 0.05), unclassified_f__Lachnospiraceae (p < 0.05), Treponema_2 (p < 0.01), and Ruminococcaceae_NK4A214_group (p < 0.01) were the main genera of gut microbiota affecting the ATTD of NDF in pigs. Christensenellaceae_R-7_group (p < 0.01), Treponema_2 (p < 0.05), Ruminococcaceae_NK4A214_group (p < 0.05), Ruminococcaceae_UCG-002 (p < 0.05), and [Eubacterium]_coprostanoligenes_group (p < 0.05) were the main genera of gut microbiota affecting the ATTD of ADF in pigs. The most important functions of the above different potential biomarkers were: carbohydrate transport and metabolism, general function prediction only, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, transcription, replication, energy production and conversion, signal transduction mechanisms, and inorganic ion transport and metabolism. The most important metabolic pathways of the above different potential biomarkers were: membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, cell motility, energy metabolism, poorly characterized, nucleotide metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling.

The core bacterial microbiome of banana (Musa spp.)

BACKGROUND

Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence 'common core' taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches. Here, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. From this experiment, we created shortlisted core 'candidates' that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies.

RESULTS

Diversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. This led to the selection of 36 'common core' bacteria, that represented 65-95% of the dominant taxa in field-grown plants and were identified as highly interconnected 'hubs' using network analysis - a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa are closely related to banana-associated bacteria observed on five other continents.

CONCLUSIONS

Our study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa, highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.

Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities

Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.

(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota

Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na⁺/H⁺ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes.

IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.

Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping

Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

Fe-based nanomaterial transformation to amorphous Fe: Enhanced alfalfa rhizoremediation of PCBs-contaminated soil

Nano-enabled phytoremediation is an emerging remediation strategy for soils that are moderately contaminated with persistent organic contaminants, and there is a significant need for increased mechanistic understanding and for case studies. Herein, we evaluated the remediation of PCB28-contaminated soil using combined alfalfa and Fe-based materials, including zero-valent iron at 20 nm, 100 nm, and 5 µm, and also iron oxide nanomaterials including α-Fe₂O₃, γ-Fe₂O₃, and Fe₃O₄ around 20-30 nm. Compared with alfalfa remediation alone (63.2%), Fe-based nanomaterials increased PCB28 removal values to 72.4-93.5% in planted soil, with α-Fe₂O₃ treatment promoting the most effective pollutant removal. Mechanistically, the crystalline Fe-based nanoparticles were transformed into amorphous forms in the plant rhizosphere, resulting in greater availability and enhanced iron nutrition. This nutritional shift induced root metabolic reprogramming of amino acid and carbohydrate cycling, and related functional bacterial enrichment of Ramlibacter, Dyella, Bacillus, and Paraburkholderia in rhizosphere. A significant positive correlation between amorphous iron and root metabolites-associated microbes with PCB28 removal was evident, implying that iron supplementation selected for rhizospheric microorganisms favored PCBs degradation. Overall, this rhizoremediation promotion strategy of Fe species-metabolites-microbes highlights the potential for the hybrid application of nano-enabled phytotechnology in the remediation of soils contaminated with persistent organic xenobiotics.

Long-term effects of liquid swine manure land surface application in an apple orchard field on soil bacterial community and heavy metal contents in apple (Malus pumila Mill.)

This study investigated the impact of liquid swine manure (LSM) land surface application in an apple orchard on soil health and copper (Cu) and zinc (Zn) in soil and apple. Three apple plots were selected, among which two for LSM application for 5 (AY5) and 11 (AY11) years with different application rates, a long-term inorganic fertilizer application plot as the control treatment (AY0). The soil and apple samples were collected for analysis of soil physicochemical properties, bacterial diversity and abundance, and the contents of Cu and Zn in soil and apple. Results showed that the LSM application significantly increased the concentration of soil nutrients with the highest in AY5, which has a high application rate of LSM. After 5 or 11 years applied, the content of total nitrogen (TN) in AY5 and AY11 increased by 125.2% and 96.7%, total phosphorus (TP) increased by 167.6% and 148.6%, and soil organic matter (SOM) increased by 180.7% and 120.6%, respectively. The AY5 treatment significantly lowered OTUs and decreased Shannon index trend with a negative correlation between soil organic matter and Shannon index. The six predominant bacterial phyla in different treatments were similar, but the LSM application significantly increased the abundance of Chloroflexi and Firmicutes. However, the abundance of Actinobacteria and Acidobacteria significantly decreased in AY5 as compared to control treatment, followed by a significant positive correlation between the abundance of Acidobacteria and soil pH. Besides, LSM application significantly increased the contents of soil Cu, Zn, and apple Zn. Overall, the results illustrated that appropriate application rate of LSM can effectively improve apple orchard soil quality and bacterial community structure, but it will increase the risk of heavy metal accumulation in soil and apples.

Effects of Continuous Cropping of Codonopsis tangshen on Rhizospheric Soil Bacterial Community as Determined by Pyrosequencing

Codonopsis tangshen, a perennial herbaceous, has been shown to be affected by continuous cropping, with significant decline in both yield and quality. In this study, we studied the effect of continuous cropping on the abundance and composition of rhizospheric soil bacterial community. Results showed that continuous cropping causes a significant decline in both yield and quality. The nutrient content in continuous cropping soil was higher than that of soil in main cropping. Pyrosequencing analyses revealed Proteobacteria and Acidobacteria as the main phyla in two types of soils. Relative abundance of Acidobacteria, Nitrospirae, TM7, and AD3 phyla was observed to be high in continuous cropping soils, whereas Chloroflexi, Bacteroidetes, and Planctomycetes phyla were richer in main cropping soils. At the genus level, high relative abundance of Pseudomonas (γ-Proteobacteria), Rhodanobacter, Candidatus Koribacter, and Candidatus were observed in continuous cropping soil. Different patterns of bacterial community structure were observed between different soils. Redundancy analysis indicated that organic matter content and available nitrogen content exhibited the strongest effect on bacterial community structure in the continuous cropping soil. Taken together, continuous cropping led to a significant decline in yield and quality, decrease in rhizospheric soil bacterial abundance, and alteration of rhizospheric soil microbial community structure, thereby resulting in poor growth of C. tangshen in the continuous cropping system.

Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes

The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of Achyranthes bidentata under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms via co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as Bacillus, Fictibacillus, Bradyrhizobium, Shinella, and Herbaspirillum. For fungi, Mortierella substituted for Fusarium in occupying an important position in different rhizocompartments under A. bidentate monoculture. Quantitative PCR analysis confirmed a significant increase in Bacillus, Pseudomonas, and Burkholderia spp. The results of the inoculation assay showed that addition of beneficial bacteria Bacillus subtilis 74 and Bacillus halodurans 75 significantly increased the root length and fresh weight of A. bidentata. Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at in vitro interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (Bacillus amyloliquefaciens 4 and B. halodurans 75) and had a negative effect on the presence of the pathogenic fungi Fusarium solani and Fusarium oxysporum. Overall, this study demonstrated that consecutive monoculture of A. bidentata can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.

Effect of co-application of Trichoderma spp. with organic composts on plant growth enhancement, soil enzymes and fungal community in soil

The application of Trichoderma spp. has the potential to reduce not only mineral fertilizer use in agriculture but also improve soil health through increased soil biological activity. Trichoderma spp. have shown potential as bio-control agents and plant growth promoting ability, but little attention has been paid to the effect of Trichoderma spp. inoculation on nutrient availability and the soil microbiome. In this study, we evaluated the effect of Trichoderma spp. inoculation on nitrogen mineralization and quantified soil enzymatic activities along with plant growth promotion potential. The influence of Trichoderma spp. and organic amendments on the soil fungal community was also investigated. For this purpose, pots and incubation experiment was carried out, and seven treatments were set as follows; poultry compost (PC), poultry compost + RW309 (PCT), cattle compost (CC), cattle compost + RW309 (CCT), rapeseed oil cake (OC), inorganic fertilizer (N) and only soil (S) were set as control. We evaluated that Trichoderma sp. RW309 produced indole-3-acetic acid, which suggested that it could contribute to plant growth enhancement during early plant growth. Inoculation of RW309 with organic materials stimulated nitrogen mineralization and increased soil phosphatase activity. Furthermore, RW309 altered the fungal community in rhizosphere soil. However, cattle compost was a more suitable culture medium for RW309 than poultry compost in terms of nitrogen mineralization, soil enzyme activity, and growth of RW309. In conclusion, Trichoderma sp. RW309 could be considered for use as a bioorganic fertilizer in combination with organic compost to minimize the use of mineral fertilizers.

Effects of phosphorus modified nZVI-biochar composite on emission of greenhouse gases and changes of microbial community in soil

The effect of modified biochar on the greenhouse gas emission in soil is not clear until now. In this study, biochar (BC) was modified by phosphoric acid (P) and further combined with nano-zero-valent iron (nZVI) to form nZVI-P-BC composite. The P modified biochar could significantly increase the available phosphorus in soil. The release of CO₂ and N₂O in soil was inhibited during the initial stage of the experiment, with inhibition becoming more obvious over time. On the contrary, CH₄ and N₂O emission in soil was enhanced by nZVI-P-BC composite. The proportion of Sphingomonas and Gemmatimonas were the most abundant bacterial species, which were related to the metabolism and transformation of nitrogen. The community structure of the fungus was also affected by nZVI-P-BC composite with Fusarium as the main species. PCoA analysis result suggested that bacterial community was more affected by the incubation time while fungal community was more related to the addition of different biochar and modified biochars.

Antagonistic Activity of Trichoderma spp. Against Fusarium oxysporum in Rhizosphere of Radix pseudostellariae Triggers the Expression of Host Defense Genes and Improves Its Growth Under Long-Term Monoculture System

Under consecutive monoculture, the abundance of pathogenic fungi, such as Fusarium oxysporum in the rhizosphere of Radix pseudostellariae, negatively affects the yield and quality of the plant. Therefore, it is pertinent to explore the role of antagonistic fungi for the management of fungal pathogens such as F. oxysporum. Our PCR-denatured gradient gel electrophoresis (DGGE) results revealed that the diversity of Trichoderma spp. was significantly declined due to extended monoculture. Similarly, quantitative PCR analysis showed a decline in Trichoderma spp., whereas a significant increase was observed in F. oxysporum. Furthermore, seven Trichoderma isolates from the R. pseudostellariae rhizosphere were identified and evaluated in vitro for their potentiality to antagonize F. oxysporum. The highest and lowest percentage of inhibition (PI) observed among these isolates were 47.91 and 16.67%, respectively. In in vivo assays, the R. pseudostellariae treated with four Trichoderma isolates, having PI > 30%, was used to evaluate the biocontrol efficiency against F. oxysporum in which T. harzianum ZC51 enhanced the growth of the plant without displaying any disease symptoms. Furthermore, the expression of eight defense-related genes of R. pseudostellariae in response to a combination of F. oxysporum and T. harzianum ZC51 treatment was checked, and most of these defense genes were found to be upregulated. In conclusion, this study reveals that the extended monoculture of R. pseudostellariae could alter the Trichoderma communities in the plant rhizosphere leading to relatively low level of antagonistic microorganisms. However, T. harzianum ZC51 could inhibit the pathogenic F. oxysporum and induce the expression of R. pseudostellariae defense genes. Hence, T. harzianum ZC51 improves the plant resistance and reduces the growth inhibitory effect of consecutive monoculture problem.

Effects of integrated biocontrol on bacterial wilt and rhizosphere bacterial community of tobacco

Bacterial wilt as a soil-borne disease was caused by Ralstonia solanacearum, and seriously damages the growth of tobacco. Integrated biocontrol method was explored to control bacterial wilt. Nevertheless, the long-term effects of the integrated biocontrol method on soil bacterial community, soil physicochemical properties and the incidence of bacterial wilt are not well understood. In this study, B. amyoliquefaciens ZM9, calcium cyanamide and rice bran were applied to tobacco fields in different ways. The disease index and incidence of tobacco bacterial wilt (TBW), soil physicochemical properties, colonization ability of B. amyoliquefaciens ZM9, and rhizopshere bacterial community were investigated. The results showed that the integrated application of B. amyoliquefaciens ZM9, rice bran and calcium cyanamide had the highest control efficiency of TBW and bacteria community diversity. Additionally, the integrated biocontrol method could improve the colonization ability of B. amyoliquefaciens ZM9. Furthermore, the integrated biocontrol method could effectively suppress TBW by regulating soil physicochemical properties, promoting beneficial bacteria and antagonistic bacteria of rhizopshere soil. This strategy has prospect of overcoming the defects in application of a single antagonistic bacteria and provides new insights to understand how to improve the colonization capacity of antagonistic bacteria and control efficacy for TBW.

Isolation of Burkholderia sp. HQB-1, A Promising Biocontrol Bacteria to Protect Banana Against Fusarium Wilt Through Phenazine-1-Carboxylic Acid Secretion

Fusarium wilt is a devastating soil-borne fungal disease caused by Fusarium oxysporum f.sp. cubense (Foc). In recent years, some antifungal bacteria have been applied for the prevention and biocontrol of pathogenic fungi. In our study, a bacterial strain HQB-1, isolated from banana rhizosphere soil, was cultured for investigation. It showed broad-spectrum antifungal activities against representative phytopathogenic fungi including Fusarium oxysporum, Colletotrichum gloeosporioides, Botrytis cinerea, and Curvularia fallax. The strain HQB-1 was identified as Burkholderia sp. by morphological, physiological, and biochemical examinations, confirmed by 16S rRNA gene sequence analysis. Among the metabolites produced by the strain, we identified an antifungal compound which was identified phenazine-1-carboxylic acid (PCA) (C₁₃H₈N₂O₂) through ultraviolet, liquid chromatography quadrupole-time of flight mass spectrometer, and nuclear magnetic response. Furthermore, PCA exhibited the lowest minimum inhibitory concentration (MIC) against F. oxysporum (1.56 μg/ml) and yielded the highest MIC against C. gloeosporioides. Pot experiments showed that application of 5 μg/ml or more of PCA efficiently controlled banana wilt and promoted the growth of banana plants. These results suggested that Burkholderia sp. HQB-1, as an important microbial resource of PCA, could be a promising biological agent against wilt diseases and promoting banana growth.

Synergistic effects of organic fertilizer and corn straw on microorganisms of pepper continuous cropping soil in China

Because of the large population, large demand, limited arable land and many environmental factors, continuous cropping have become a very common phenomenon in China. However, long-term continuous cropping has caused a series of serious soil-borne diseases, and the yield and quality of crops to drop, which seriously restricted the sustainable development of agricultural industry. Therefore, in order to improve the yield of pepper and reduce the occurrence of soil-borne diseases, it is essential to understand the effect of continuous cropping of pepper on soil microbial community composition and abundance. In this study, high throughput sequencing was used to study the effects of seven treatments of organic fertilizers and corn straw on soil microbial community and function of pepper continuous cropping. The results showed that the yield of all treatments was significantly higher than that of the control. The soil microbial diversity and community composition showed that Proteobacteria and Ascomycota were the most abundant phylum in all treatments. In conclusion, there were significant differences among the seven treatments and the treatment of fowl dung with corn straw was the best fertilizer combination to improve the yield and output value of pepper. Besides, the addition of fowl dung and corn straw not only can improve the community and functions of microorganisms, but also enhance the ability of disease resistance, and ultimately decrease the soil-borne diseases. The results will help to provide scientific basis for rational application of organic fertilizer and corn straw, and overcoming continuous cropping obstacles.

Effects of organic fertilizer on soil nutrient status, enzyme activity, and bacterial community diversity in Leymus chinensis steppe in Inner Mongolia, China

The long-term impact of human exploitation and environmental changes has led to a decline in grassland productivity and soil fertility, which eventually results in grassland degradation. The application of organic fertilizer is an effective improvement measure; however, it is still not fully understood how the addition of organic fertilizer influences grassland soil fertility and plant composition. A set of experiments were conducted in Inner Mongolia in China to reveal the tradeoff between steppe plants and soil microorganisms and the eco-physiological mechanisms involved, and how the addition of vermicompost and mushroom residues affect microbial diversity, enzyme activities, and the chemical properties of soil in degraded Leymus chinensis grassland. Organic fertilizer improved the soil nutrient status and shaped distinct bacterial communities. Compared with the control the available phosphorus (AP) and available potassium (AK) contents were highest under treatments a3 and b3, and the aboveground biomass was highest under the b3 treatment. Soil sucrase activities increased by 7.88% under the b3 treatment. Moreover, the richness index significantly increased by 7.07% and 7.23% under the a1 and b2 treatments, respectively. The most abundant Actinobacteria and Proteobacteria were detected in the organic fertilizer treatment. A linear discriminant analysis effect size (LEfSe) indicated that the bacterial community was significantly increased under the b3 treatment. A canonical correspondence analysis (RDA) and spearman correlation heatmap confirmed that total P (TP) and urease were the key driving factors for shaping bacterial communities in the soil. Our results indicated that the application of large amounts of vermicompost and mushroom residues increased the availability of nutrients and also enhanced the biodiversity of soil bacterial communities in L. chinensis grasslands, which will contribute to the sustainable development of agro-ecosystems.

Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation

Background

Different mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community structure and ecosystem function in tea plantation under different mulching patterns was limited. In this study, we investigated bacterial and fungal communities of tea plantation soils under polyethylene film and peanut hull mulching using high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing.

Results

The results showed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, and the dominant fungal phyla were Ascomycota, Mortierellomycota and Basidiomycota in all samples, but different mulching patterns affected the distribution of microbial communities. At the phylum level, the relative abundance of Nitrospirae in peanut hull mulching soils (3.24%) was significantly higher than that in polyethylene film mulching soils (1.21%) in bacterial communities, and the relative abundances of Mortierellomycota and Basidiomycota in peanut hull mulching soils (33.72, 21.93%) was significantly higher than that in polyethylene film mulching soils (14.88, 6.53%) in fungal communities. Peanut hull mulching increased the diversity of fungal communities in 0–20 cm soils and the diversity of bacterial communities in 20–40 cm soils. At the microbial functional level, there was an enrichment of bacterial functional features, including amino acid transport and metabolism and energy production and conversion, and there was an enrichment of fungal functional features, including undefined saprotrophs, plant pathogens and soils aprotrophs.

Conclusions

Unique distributions of bacterial and fungal communities were observed in soils under organic mulching. Thus, we believe that the organic mulching has a positive regulatory effect on the soil bacterial and fungal communities and ecosystem functions, and so, is more suitable for tea plantation.

Deep tillage combined with biofertilizer following soil fumigation improved chrysanthemum growth by regulating the soil microbiome

Sustained monoculture often leads to the inhibition of plant growth, the decrease of the soil microbial diversity, and changes in soil microbial community composition, particularly to the accumulation of soil‐borne pathogens. In this study, we conducted field experiments to investigate the practical effects of tilling the soil down to a depth of 40 cm (40dp) in combination with dazomet (D) soil fumigation and/or the application of a bio‐organic fertilizer (B) on chrysanthemum growth, with a focus on the potential mechanisms underlying the responses of the soil microbiome. The growth indices of chrysanthemum were significantly (p < .05) increased in the DB + 40dp treatment compared to that in other treatments. The weighted and unweighted UniFrac distances in the principal coordinate analysis (PCoA) revealed that soil bacterial and fungal community compositions were separated according to the treatments. The abundance of genera potentially expressing growth promotion, such as Pseudomonas and Bacillus, was increased in the DB + 40dp treatment. In addition, the combined DB + 40dp treatment enhanced the activities of catalase, urease, sucrase, and β‐d‐glucosidase, and significantly increased the levels of available nitrogen, phosphorus, and potassium in the soil. The redundancy analysis (RDA) implied that the composition of the microbiome was correlated to soil enzymatic activities and soil potassium availability in the rhizosphere soil of chrysanthemum plants. Our findings suggest that the DB + 40dp treatment is a better strategy for improving chrysanthemum growth and regulating the rhizosphere microbiome in monoculture soils than the methods presently employed by commercial chrysanthemum producers.

Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.

Different effects of soil bacterial communities affected by biocontrol agent YH-07 on tomato Fusarium wilt inhibition

The model plant tomato was used to verify the effect and mechanism of a novel discovered strain YH-07 which is a potential agent for biological control of soil borne disease named tomato Fusarium wilt.

Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture

To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.

Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests

Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.

Comparative Transcriptome Analysis Reveals the Biocontrol Mechanism of Bacillus velezensis F21 Against Fusarium Wilt on Watermelon

The watermelon (Citrullus lanatus) is one of the most important horticultural crops for fruit production worldwide. However, the production of watermelon is seriously restricted by one kind of soilborne disease, Fusarium wilt, which is caused by Fusarium oxysporum f. sp. niveum (Fon). In this study, we identified an efficient PGPR strain B. velezensis F21, which could be used in watermelon production for Fon control. The results of biocontrol mechanisms showed that B. velezensis F21 could suppress the growth and spore germination of Fon in vitro. Moreover, B. velezensis F21 could also enhance plant basal immunity to Fon by increasing the expression of plant defense related genes and activities of some defense enzymes, such as CAT, POD, and SOD. To elucidate the detailed mechanisms regulating B. velezensis F21 biocontrol of Fusarium wilt in watermelon, a comparative transcriptome analysis using watermelon plant roots treated with B. velezensis F21 or sterile water alone and in combination with Fon inoculation was conducted. The transcriptome sequencing results revealed almost one thousand ripening-related differentially expressed genes (DEGs) in the process of B. velezensis F21 triggering ISR (induced systemic resistance) to Fon. In addition, the Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that numerous of transcription factors (TFs) and plant disease resistance genes were activated and validated by using quantitative real-time PCR (qRT-PCR), which showed significant differences in expression levels in the roots of watermelon with different treatments. In addition, genes involved in the MAPK signaling pathway and phytohormone signaling pathway were analyzed, and the results indicated that B. velezensis F21 could enhance plant disease resistance to Fon through the above related genes and phytohormone signal factors. Taken together, this study substantially expands transcriptome data resources and suggests a molecular framework for B. velezensis F21 inducing systemic resistance to Fon in watermelon. In addition, it also provides an effective strategy for the control of Fusarium wilt in watermelon.

Characteristics of Gut Microbiota in Sows and Their Relationship with Apparent Nutrient Digestibility

The gut microbiota plays important roles in animal health and nutrient digestibility. The characteristics of gut microbiota population in grower pigs and their correlation with apparent nutrient digestibility were assessed in previous study. Here we studied characteristics of intestinal microbiota of sows and analyzed their relationships with apparent nutrient (ether extract (EE), crude protein (CP), crude fiber (CF), neutral detergent fiber (NDF) and acid detergent fiber (ADF)) digestibility. Firmicutes and Bacteroidetes were the most dominant phyla, approximately 73% of the total sequences. Treponema, Oscillibacter and Lactobacillus were the most dominant generas, more than 49% of the total sequences. The microbiota of sows clustered separately from the microbiota of grower pigs at the age of D28 D60, D90 and D150. The abundance of Clostridium and Turicibacter was positively correlated with apparent EE digestibility. The abundance of Anaerofustis and Robinsoniella in sow fecal samples was positively correlated with apparent CF digestibility. The abundance of Collinsella and Sutterella was positively correlated with apparent NDF digestibility. The abundance of Clostridium, Collinsella, Robinsoniella and Turicibacter was positively correlated with apparent ADF digestibility. Sows have their unique gut microbial structure compared with grower pigs and some of them participate in the digestive process of different nutrients.

Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils

Plant health is determined by the comprehensive effect of soil physicochemical and biological properties. In this study, we compared the chemical properties and microbiomes of the rhizosphere soils of healthy, Fusarium oxysporum-infected, and dead watermelon plants and attempted to assess their potential roles in plant health and Fusarium wilt expression. The rhizosphere soils were collected from watermelon plants grown in a greenhouse under the same field management practices, and various soil microbial and chemical characteristics were analyzed. The rhizosphere soil of healthy plants had the lowest abundance of F. oxysporum and pH and the highest contents of ammonium (NH₄⁺) and nitrate (NO₃^-). The relative content of hemicellulose was decreased in the rhizosphere soil of F. oxysporum-infected plants. The differences in soil microbial compositions among the watermelons at the three health statuses were obvious, and their microbiomes changed gradually along with plant health status. The microbiome in the rhizosphere soil of healthy plants had the highest relative abundances of potential antagonists and the lowest relative abundances of potential pathogens. The specific microbial composition together with some chemical properties of the rhizosphere soil of healthy plants might be responsible for inhibiting Fusarium wilt expression.

Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China

Bacteria, as the key component of soil ecosystems, participate in nutrient cycling and organic matter decomposition. However, how fertilization regime affects the rhizospheric bacterial community of reddish paddy soil remains unclear. Here, a long-term fertilization experiment initiated in 1982 was employed to explore the impacts of different fertilization regimes on physicochemical properties and bacterial communities of reddish paddy rhizospheric soil in Central South China by sequencing the 16S rRNA gene. The results showed that long-term fertilization improved the soil nutrient status and shaped the distinct rhizospheric bacterial communities. Particularly, chemical NPK fertilizers application significantly declined the richness of the bacterial community by 7.32%, whereas the application of manure alone or combined with chemical NPK fertilizers significantly increased the biodiversity of the bacterial community by 1.45%, 1.87% compared with no fertilization, respectively. Moreover, LEfSe indicated that application of chemical NPK fertilizers significantly enhanced the abundances of Verrucomicrobia and Nitrospiraceae, while manure significantly increased the abundances of Deltaproteobacteria and Myxococcales, but the most abundant Actinobacteria and Planctomycetes were detected in the treatment that combined application of manure and chemical NPK fertilizers. Furthermore, canonical correspondence analysis (CCA) and the Mantel test clarified that exchangeable Mg2+ (E-Mg2+), soil organic carbon (SOC) and alkali-hydrolyzable nitrogen (AN) are the key driving factors for shaping bacterial communities in the rhizosphere. Our results suggested that long-term balanced using of manure and chemical fertilizers not only increased organic material pools and nutrient availability but also enhanced the biodiversity of the rhizospheric bacterial community and the abundance of Actinobacteria, which contribute to the sustainable development of agro-ecosystems.

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing

Soil bacteria play key roles in determining soil health and plant growth. In this study, four sweet potato fields that had been consecutively monocultured for 1, 2, 3, and 4 years were used to investigate the effect of monoculture on soil physicochemical properties and soil bacterial communities. The results revealed that continuous cropping led to a significant decline in soil pH, soil organic carbon, and soil bacterial abundance. Miseq pyrosequencing analysis of 16S rRNA genes revealed that Proteobacteria and Bacteroidetes were the main phyla in the sweet potato monoculture soils, comprising up to 66.24% of the total sequences. The relative abundances of beneficial bacteria, including Actinobacteria, Gemmatimonadetes, Firmicutes, Xanthomonadaceae, Rhodospirillaceae, and Syntrophobacteraceae, as well as their subgroups at the genus and operational taxonomic unit (OTU) levels, decreased considerably as the number of continuous cropping years increased. In contrast, the number of potentially pathogenic bacteria, such as Acidobacteria, Sphingomonadaceae, and Pedobacter accumulated with increasing years. The results also showed the alterations to the bacterial community in the sweet potato monoculture soils were mainly driven by soil pH and soil organic matter. Overall, the decline in soil quality after successive sweet potato monoculture can be attributed to the imbalance in soil properties and soil microbes, including the decrease in soil pH and soil organic carbon, and the enrichment of pathogenic bacteria at the expense of plant-beneficial bacteria.

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region

Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.

Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27

N₂O-reducing organisms with nitrous oxide reductases (NosZ) are known as the only biological sink of N₂O in the environment. Among the most abundant nosZ genes found in the environment are nosZ genes affiliated with the understudied Gemmatimonadetes phylum. In this study, a unique regulatory mechanism of N₂O reduction in Gemmatimonas aurantiaca strain T-27, an isolate affiliated with the Gemmatimonadetes phylum, was examined. Strain T-27 was incubated with N₂O and/or O₂ as the electron acceptor. Significant N₂O reduction was observed only when O₂ was initially present. When batch cultures of strain T-27 were amended with O₂ and N₂O, N₂O reduction commenced after O₂ was depleted. In a long-term incubation with the addition of N₂O upon depletion, the N₂O reduction rate decreased over time and came to an eventual stop. Spiking of the culture with O₂ resulted in the resuscitation of N₂O reduction activity, supporting the hypothesis that N₂O reduction by strain T-27 required the transient presence of O₂ The highest level of nosZ transcription (8.97 nosZ transcripts/recA transcript) was observed immediately after O₂ depletion, and transcription decreased ∼25-fold within 85 h, supporting the observed phenotype. The observed difference between responses of strain T-27 cultures amended with and without N₂O to O₂ starvation suggested that N₂O helped sustain the viability of strain T-27 during temporary anoxia, although N₂O reduction was not coupled to growth. The findings in this study suggest that obligate aerobic microorganisms with nosZ genes may utilize N₂O as a temporary surrogate for O₂ to survive periodic anoxia.IMPORTANCE Emission of N₂O, a potent greenhouse gas and ozone depletion agent, from the soil environment is largely determined by microbial sources and sinks. N₂O reduction by organisms with N₂O reductases (NosZ) is the only known biological sink of N₂O at environmentally relevant concentrations (up to ∼1,000 parts per million by volume [ppmv]). Although a large fraction of nosZ genes recovered from soil is affiliated with nosZ found in the genomes of the obligate aerobic phylum Gemmatimonadetes, N₂O reduction has not yet been confirmed in any of these organisms. This study demonstrates that N₂O is reduced by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27, and suggests a novel regulation mechanism for N₂O reduction in this organism, which may also be applicable to other obligate aerobic organisms possessing nosZ genes. We expect that these findings will significantly advance the understanding of N₂O dynamics in environments with frequent transitions between oxic and anoxic conditions.

Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.

Insights into the Regulation of Rhizosphere Bacterial Communities by Application of Bio-organic Fertilizer in Pseudostellaria heterophylla Monoculture Regime

The biomass and quality of Pseudostellariae heterophylla suffers a significant decline under monoculture. Since rhizosphere miobiome plays crucial roles in soil health, deep pyrosequencing combined with qPCR was applied to characterize the composition and structure of soil bacterial community under monoculture and different amendments. The results showed compared with the 1st-year planted (FP), 2nd-year monoculture of P. heterophylla (SP) led to a significant decline in yield and resulted in a significant increase in Fusarium oxysporum but a decline in Burkholderia spp. Bio-organic fertilizer (MT) formulated by combining antagonistic bacteria with organic matter could significantly promote the yield by regulating rhizosphere bacterial community. However, organic fertilizer (MO) without antagonistic bacteria could not suppress Fusarium wilt. Multivariate statistics analysis showed a distinct separation between the healthy samples (FP and MT) and the unhealthy samples (SP and MO), suggesting a strong relationship between soil microbial community and plant performance. Furthermore, we found the application of bio-organic fertilizer MT could significantly increase the bacterial community diversity and restructure microbial community with relatively fewer pathogenic F. oxysporum and more beneficial Burkholderia spp. In conclusion, the application of novel bio-organic fertilizer could effectively suppress Fusarium wilt by enriching the antagonistic bacteria and enhancing the bacterial diversity.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.

Dynamic distribution of the gut microbiota and the relationship with apparent crude fiber digestibility and growth stages in pigs

The gut microbiota plays an important role in nutrient digestibility in animals. To examine changes in the pig gut microbiota across growth stages and its effects on nutrient digestion, the gut microbiota population in pigs at 28 days (before weaning), and 60, 90, and 150 days of age was assessed by 16S rDNA gene sequencing. The apparent digestibility of crude fiber (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein (CP) and ether extract (EE) was also assessed in these pigs. A total of 19,875 operational taxonomic units (OTUs) were identified from all samples. Both bacterial abundance and diversity increased with age. A total of 22 phyla and 249 genera were identified from all fecal samples; Firmicutes and Bacteroidetes were the most dominant phyla in all samples. With increasing age, the proportion of TM7 and Tenericutes increased, whereas the proportion of Lentisphaerae and Synergistetes decreased. The abundance of 36 genera varied with age, and the apparent digestibility of CF increased with age. Three phyla, Proteobacteria, Tenericutes and TM7, and 11 genera, including Anaeroplasma, Campylobacter, and Clostridium, were correlated with apparent CF digestibility.