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Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and poorly understood in natural rhizosphere microbiomes. We studied biocontrol efficacy of different phage combinations on Ralstonia solanacearum infection in tomato. Increasing the number of phages in combinations decreased the incidence of disease by up to 80% in greenhouse and field experiments during a single crop season. The decreased incidence of disease was explained by a reduction in pathogen density and the selection for phage-resistant but slow-growing pathogen strains, together with enrichment for bacterial species that were antagonistic toward R. solanacearum. Phage treatment did not affect the existing rhizosphere microbiota. Specific phage combinations have potential as precision tools to control plant pathogenic bacteria. Phage combination therapies reduce bacterial wilt disease incidence in tomato by up to 80%. [ABSTRACT FROM AUTHOR]

Aims: To investigate the ability of higher nitrogen (N) use efficiency (NUE) in rice production to achieve higher grain yields by optimal N management (OPT). Methods: In 2012 and 2013, four field experiments were conducted in Liyang and Rugao counties, Jiangsu Province, China to investigate the ability of the N-nutrient index (NNI) to mediate the effects of N-free control (CK), farmers' fertilizer practice (FFP), and OPT N management methods on grain yield and NUE through regulating the leaf functions of rice. Results: Compared with FFP, the average rice yield and NUE for OPT were increased, while the N rate was reduced. NNI showed a dynamic change that reached an optimal status in OPT at the harvest stage. N management had a remarkable effect on the leaf area index (LAI), with OPT mitigating the differences between leaf positions, such that basal leaf LAI was improved to compensate for the decreased LAI of the top three leaves. During the grain-filling process, the top three leaves exhibited higher net photosynthesis rate (Pn) and higher grain weights and shorter grain-filling periods of both superior and inferior spikelets in OPT. Based on the contribution of different organs to grain production from the heading to harvest stage, two strategies of yield formation were observed, in which OPT enhanced the dependence on the stems (stem, sheath, and other leaves), while FFP was more dependent on the top three leaves. Conclusions: Our results indicate that optimizing N application improves NNI and leaf functions to increase rice yield and NUE. [ABSTRACT FROM AUTHOR]

Characterizing the rhizosphere microbial community composition associated with enhanced crop yield is an important first step towards understanding the role of the microbiota in soil fertility. In the present study, we conducted a two-seasons field experiment in a maize-cabbage cropping system under chemical (CF), organic (OF) and bio-organic (BOF) fertilizer regimes as a model to investigate the combinatory effect of fertilizer treatment and crop type on rhizosphere soil microbiota by targeted sequencing of both the bacterial and fungal communities. The two-seasons sustainable application of bio-organic fertilizer (BOF) containing Trichoderma effectively increased maize and cabbage yields, whereas organic fertilizer (OF) increased but not significant, compared to the application of chemical fertilizer (CF). Both fertilizer treatment and crop type induced a significant effect on soil physiochemical properties and were the major factors that impacted the composition of the rhizosphere soil microbiome. Relative abundances of Trichoderma were significantly enhanced in the BOF treatment, compared to the OF and CF treatments, and exhibited significant positive relationships with crop yield improvement. The application of bio-organic fertilizer may enhance the growth promotion effect of Trichoderma and increase the abundance of potentially beneficial microbial groups such as the genera Cladorrhinum and Massilia , which were found to be highly correlated to increased crop yields. Overall, the influence of bio-organic fertilizer on crop yield is proposed to be through mechanisms by introduction of the target strain NJAU 4742 and stimulation of a potentially beneficial microbial consortia, in combination with alterations in fungal and bacterial composition and abundance, leading to an enhancement in crop yield. • Bio-organic fertilizer containing Trichoderma increased maize and cabbage yields. • Crop type and fertilizer treatment were the major factors influenced rhizosphere microbiome. • Organic amendments affected the microbial alpha and beta diversities. • Trichoderma played an important role in crop yield enhancement. • Potentially induced beneficial microbial groups are associated with increased yields. [ABSTRACT FROM AUTHOR]

Leaf surface fertilization with liquid fertilizer produced from amino acids constitutes a potentially important source of nitrogen and is important for plant production. However, few reports have focused on the plant growth promotion by novel liquid fertilizers created by new amino acid resources, let alone the influence on leaf microbiota. In this study, the effects of liquid fertilizer, created by amino acids hydrolyzed from animal hairs with or without the PGPR strain Bacillus amyloliquefaciens SQR9, on crop yield and leaf microbiota were investigated. The results showed that leaves sprayed with amino acid liquid fertilizer (AA) and liquid biological fertilizer (AA9) persistently increased cowpea yields compared to the control amended with chemical fertilizer (CF). Fertilization with amino acid fertilizer showed no significant difference in microbial composition compared with the CF treatment; however, the introduction of functional microbes altered the microbial composition. Pearson correlation analysis, VPA analysis and SEM models all revealed that the amino acids liquid fertilizer application, but not the functional strain or the altered microbiota, performed as the direct driver attributing to yield enhancement. We conclude that leaf fertilization with a novel amino acid liquid fertilizer can greatly enhance the crop yield and that the addition of beneficial microbes may perform the role in further altering the composition of leaf microbiota. [ABSTRACT FROM AUTHOR]

Summary: Rhizobacteria devote a relatively large percentage of their genomes to encode bioactive natural products that are important for competition in the rhizosphere. In this study, a plant beneficial rhizobacterium Bacillus velezensis SQR9 was discovered to produce novel antibacterial fatty acids, Bacillunoic acids, which are encoded on a genomic island (GI). This GI contains a hybrid type I fatty acid synthase (FAS)‐polyketide synthase (PKS) system and an ABC transporter. The FAS was predicted to synthesize a primer that was transferred to the PKS to synthesize Bacillunoic acids. The synthesized Bacillunoic acids inhibit the growth of diverse bacteria, with the strongest activity against closely related Bacillus strains, the ABC transporter exported the toxic Bacillunoic acids upon their induction for protecting the producing strain. The inhibition of other Bacillus strains by Bacillunoic acids extended the antimicrobial spectrum of SQR9 and enhanced its competition with closely related root‐associated bacteria. So, through the obtaining of this GI by horizontal gene transfer, strain SQR9 not only acquired a competitive weapon but also acquired a self‐protecting shield, which increased its competition with other rhizobacteria. [ABSTRACT FROM AUTHOR]

Summary: When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin‐encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H2O2), which is stored in microscopic bag‐like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H2O2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H2O2 in signalling and fungal communication. [ABSTRACT FROM AUTHOR]

Fusarium wilt of watermelon caused by Fusarium oxysporums f. sp. niveum (FON) is the most destructive disease impacting production. Soil fumigation using ammonium bicarbonate coupled with bioorganic fertilizer (BOF) application was conducted in the field in order to suppress Fusarium wilt disease. The composition of the soil microbiome after fumigation and at harvest was assessed using MiSeq high throughput sequencing. Soil fumigation succeeded in suppressing disease incidence, with a drop from 96% to <40%, with the addition of lime boosting suppression by a further ~12%. The addition of BOF also contributed to disease suppression by increasing the control efficacy from 7% to 12%. Alterations in the bacterial and fungal community composition was primarily driven by fumigation followed by fertilization. The abundance of the total microbial community also exhibited a positive influence on the survival certain of microbial populations after fumigation. Fumigation strongly suppressed soil pathogen abundance while both lime and BOF addition enhanced the suppression effect. In total, stronger fumigation resulted in a partial collapse of the indigenous microbial community with an anti-phytopathogenic re-structured community arising due to the application of bio-organic fertilizer. [ABSTRACT FROM AUTHOR]

Plant-beneficial microbes improve while pathogens reduce plant performance. When introduced in soils, such microbes can induce entire microbiome changes. However, the impact of those microbial introductions on protists – key predators within the soil microbiome – remain unknown. Here, we tracked how soil protists respond to bacterial (Bacillus and Ralstonia) and fungal (Trichoderma and Fusarium) introductions, with both microbial groups represented by one beneficial and one pathogenic taxon. We found that plant-beneficial Bacillus bacteria change the protist community structure. This community-shift was likely induced by an increased fungi/bacteria ratio, supported by a negative correlation of the fungi/bacteria ratio with the relative abundance of phagotrophic protists across all treatments. Our results indicate that microbial introductions can impact protist communities, thereby altering microbiome-derived multi-functionality. • We tested how bacterial and fungal species introductions affect soil protists. • Introduced Bacillus bacteria changed the protist community. • Phagotrophic protists were negatively correlated with the fungi/bacteria ratio. [ABSTRACT FROM AUTHOR]

Background and aims: The increasing input of anthropogenically-derived nitrogen (N) to ecosystems raises a crucial question: how do N inputs modify the soil microbial stability, and thus affect crop productivity? Methods: Soils from an 8-year rice-wheat rotation experiment with increasing N-input rates were subjected to drying–rewetting (DW) cycles for investigating the resistance and resilience of soil functions, in terms of abundances of genes (potential functions) and activities of enzymes (quantifiable functions), to this stress, and particularly the contribution of resistance and resilience on crop production was evaluated. Results: Although the DW cycles had a stronger effect compared to N fertilization level, the N input was also important in explaining the variation in the resistance and resilience of functional genes and the activities of enzymes involved in C, N and P cycling. Crop yields benefited from both of high resistance and high resilience of soil microbial functions, though the resistance and resilience of soil enzyme activities exhibited a stronger contribution to crop yields compared to the functional genes and the overall contribution strength was conditioned by N input levels. Conclusions: In addition to the well-known direct contribution of N fertilization on crop yields, N input plays an indirect role on crop production via conditioning the resistance and resilience of soil functions in response to repeated DW cycles. [ABSTRACT FROM AUTHOR]

[Display omitted] • A comprehensive investigation of antibiotic resistance genes (ARGs) in compost. • The potential risk of ARGs in compost lies between manure and soil. • The metabolic interactions dominated by antibiotic-resistant bacteria might intensify the transfer of ARGs. In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing. [ABSTRACT FROM AUTHOR]

Typical symptoms of potassium deficiency, characterized as chlorosis or withered necrosis, occur concomitantly with downregulated photosynthesis and impaired leaf water transport. However, the prominent limitations and mechanisms underlying the concerted decreases of leaf photosynthesis and hydraulic conductance are poorly understood. Monocots and dicots were investigated based on responses of photosynthesis and hydraulic conductance and their components and the correlated anatomical determinants to potassium deficiency. We found a conserved pattern in which leaf photosynthesis and hydraulic conductance concurrently decreased under potassium starvation. However, monocots and dicots showed two different hydraulic‐redesign strategies: Dicots tended to show a decreased minor vein density, whereas monocots reduced the size of the bundle sheath and its extensions, rather than the minor vein density; both of these strategies may restrain xylem and outside‐xylem hydraulic conductance. Additionally, potassium‐deprived leaves developed with fewer mesophyll cell‐to‐cell connections, leading to a reduced area being available for liquid‐phase flow. Further quantitative analysis revealed that mesophyll conductance to CO2 and outside‐xylem hydraulic resistance were the major contributors to photosynthetic limitation and increased hydraulic resistance, at more than 50% and 60%, respectively. These results emphasize the importance of potassium in the coordinated regulation of leaf photosynthesis and hydraulic conductance through modifications of leaf anatomy. This work provides the first hints that monocots and dicots have two different hydraulic‐redesign strategies for the modulation of leaf venation and mesophyll traits in managing the coordination of leaf hydraulic conductance and photosynthesis under prolonged potassium deficiency. [ABSTRACT FROM AUTHOR]

Abstract Soil microorganisms play an essential role in the redistribution of soil aggregate sizes due to the microenvironmental changes, but little is known about the changes in microbial communities (especially fungi) and their activities within different microenvironments due to agronomic managements. Here, we examined the influence of fertilization (inorganic and inorganic plus organic amendments) on soil aggregate distribution and the microbial communities within aggregates at the site of a long-term fertilization experiment. Significant impacts on soil aggregate distribution and distinct changes in fungal and bacterial communities in soil aggregates due to fertilization were observed, with the fungal community exhibiting more marked changes compared with the bacterial community. Soil carbon and nitrogen contents in aggregates were the most closely related to changes in microbial communities associated with soil aggregates. The changes of microbial taxa abundance in aggregates were generally accompanied by the redistributions of these taxa among all size aggregates, showing the preference for specific ecological niches for these taxa under fertilizations. Both applications of nitrogen alone (N) and inorganic plus organic amendment (NPKM) contributed to mega-aggregate formation. N treatment caused the low total fungal counts in mega-aggregates and carbon depletion, whereas it increased the abundance of N 2 O-producing fungi in both mega- and macro-aggregates, denitrifying bacteria in micro-aggregates and nitrifying bacteria in macro-aggregates. In contrast, NPKM treatment mitigated/prevented the sharp shifts of the abundance of these microbes mentioned above with nitrogen fertilization, and increased the ectomycorrhizal fungi abundance in all soil fractions as well as carbon accumulation in soil. Our results suggest that the responses of soil bacteria and fungi to fertilizations are modified by their ecological niches, which responses are responsible for the variation of ecosystem services. Highlights • Fertilizations changed distinctly fungal vs. bacterial community in soil aggregates. • Fertilizations caused shifts between enrichment and depletion of taxa in aggregates. • NPKM could reverse the microbial communities in aggregate under N application alone. • Soil C and N stores in aggregates closely affected microbial communities. [ABSTRACT FROM AUTHOR]

Aims: Plant growth-promoting rhizobacteria (PGPR) substantially improve plant growth and health, but their effects on the succession of rhizosphere microbiota throughout the growth period triggered by pre-inoculation have not yet been considered. Methods: Pepper seedlings cultured from a bio-nursery substrate containing Bacillus velezensis NJAU-Z9 and ordinary nursery substrate were used in this study to evaluate the effects of pre-colonization of a PGPR strain at the seedling stage on yield enhancement. To elucidate the underlying mechanisms involved in the rhizosphere microbiota succession during the whole growth period and their association with yield enhancement, high-throughput sequencing combined with qPCR was conducted. Results: The results showed that, compared to the control without inoculation, pre-inoculation led to a steady yield enhancement in two-season field trials, as well as higher rhizosphere bacterial richness (Chao1) and diversity (Shannon-Wiener). The plant growth stage as the first driving factor, followed by pre-colonization drove the variations of the rhizosphere microbial community composition according to multivariate regression tree analysis and principal coordinate analysis. Variance partitioning analysis (VPA) and Mantel test results showed that the previous plant growth period induced variations in the fungal and bacterial communities at the next stage. Compared to the seedling and flowering stages, the mature-stage microbial community showed a higher degree of explanation of yield enhancement. Additionally, pre-inoculation led to distinctive rhizosphere microbiota succession compared to the control, due to alteration of the initial community. The heat map analysis showed that the rhizosphere microbiota was related to crop yield. In addition to Bacillus velezensis NJAU-Z9, which showed stable abundance in the pepper rhizosphere, stable higher relative abundance of the bacterial genera Sphingomonas, Sphingopyxis, Bradyrhizobium, Chitinophaga, Dyadobacter, Streptomyces, Lysobacter, Pseudomonas and Rhizomicrobium, and the fungal genera Cladorrhinum, Cladosporium and Aspergillus throughout the growth period induced by pre-colonization was associated with yield enhancement. Conclusions: Overall, we conclude that pre-colonization with PGPR changed the initial rhizosphere microbiota and that the plant was triggered to further select distinctive microbes to form unique rhizosphere microbial consortia at the later growth stages, which resulted in plant growth promotion. [ABSTRACT FROM AUTHOR]

Abstract Knowledge of organic matter transformation under simulated rapid composting is essential for the understanding of biodegradation processes. Herein, several technologies, including atomic force microscope (AFM), X-ray photoelectron spectroscopy (XPS) and 13C Nuclear Magnetic Resonance Spectroscopy (13C NMR) were used to gain insight of the composition and architecture of the substrate during biodegradation. The total carbon of the substrate was decreased by 27.7% compared to the initial content, while the total nitrogen was increased from 1.1% to 1.8% at the end. The water soluble carbon, water soluble nitrogen and hydrolytic enzyme activities fluctuated strongly between 3 and 14 days, which was considered as the active stage of the composting process. The appearance of microfibers and deep ditch indicated that the tunneling might be one of the mechanisms of the composting microorganisms to degrade the lignocellulose. The X-ray photoelectron spectroscopy (XPS) analysis results showed that the main degradable carbon component was C1 (containing C-H or C-C bonds), which was decreased by 25.5% compared to the initial substrate. The 13C NMR analysis showed that the O-alkyl-C group dominated the resonance signals in all treatments ranging from 76.6% to 83.1% and alkyl-C fluctuated from 8.1% to 10.2%, indicating the effective degradation of lignocellulose. In summary, the combination of morphological observations by atomic force microscope (AFM) and the chemical analysis by XPS and 13C NMR is a promising approach for the characterization of agricultural wastes biodegradation process. Graphical abstract Image 10181 [ABSTRACT FROM AUTHOR]

Antibiosis and resource competition are major drivers shaping the assembly, diversity and functioning of microbial communities. While it is recognized that competition is sensitive to environmental conditions, it is unclear to what extent this mediated by the availability of different carbon resources.Here, we used a model laboratory system to directly test this by exploring how carbon resource richness and identity shape resource competition and antibiosis between plant probiotic Bacillus amyloliquefaciens and phytopathogenic Ralstonia solanacearum bacteria. We found that while sugars typically promoted B. amyloliquefaciens growth, organic and amino acids increased the production of both bacillaene and macrolactin antibiotics and the direct inhibition of R. solanacearum. In contrast, when multiple different carbon resources were available, B. amyloliquefaciens could efficiently grow and produce antibiotics at the same time.Together, these results suggest that high carbon resource richness allows concurrent expression of growth‐ and antibiosis‐related traits, potentially altering bacterial competitive dynamics and plant growth promotion in microbial communities. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Aims: Continuous cropping of watermelon is known to result in the disruption of the rhizospheric bacteria and fungi that contribute to the occurrence of Fusarium wilt disease. However, the underlying changes in microbial composition and function as a response to mono-cropping are less studied. Methods: In this study, differences in composition and potential function of the microbiome between healthy and diseased soils were investigated using MiSeq targeted sequencing and the functional GeoChip array, respectively. Results: Twenty years of continuous watermelon monoculture was found to significantly alter the soil microbial communities by increasing bacterial diversity but decreasing fungal diversity. Compare to bacterial network, fungal co-occurrence networks were less robust and less connected in the monoculture diseased soil. Identified keystone species, belonging to the Proteobacteria, Bacteroidetesand Acidobacteria, were present in both the diseased and healthy soils. Key fungal species from the healthy soil belonged solely within the Ascomycete, while in the diseased soil Basidiomycota were dominant. As such, overall variations in the composition of the soil microbiome are accompanied by changes in the identities of the keystone species when comparing healthy versus diseased soils, further suggesting that soil function may also be altered. Relative abundances of genes associated with the degradation of hemicelluloses and chitin, the Calvin circle, ammonification, stress responses, iron uptake, and nitrogen fixation were significantly higher under long-term monoculture. Particularly, Fusarium spp. relative abundance was positively correlated with the relative abundances of genes involved in adherence, cellular metabolism, and immune evasion which may facilitate pathogen infection of plant roots. Conclusions: In conclusion, these results highlight the significant compositional and functional differences in microbial communities between Fusarium wilt diseased soils and healthy soils under watermelon cultivation. This provides insight into the complex array of microorganisms in soils that suffer from Fusarium disease and illustrates potential directions towards the manipulation of the soil microbiome for suppression of this disease. [ABSTRACT FROM AUTHOR]

Summary: Chemoautotrophic ammonia‐oxidizers and nitrite‐oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long‐term fertilization regimes remain largely under‐investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia‐oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira‐like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long‐term fertilization shifted the composition of active Nitrospira‐like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential. [ABSTRACT FROM AUTHOR]

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities. [ABSTRACT FROM AUTHOR]

Summary: Chemotaxis to plant root exudates is supposed to be a prerequisite for efficient root colonization by rhizobacteria. This is a highly multifactorial process since root exudates are complex compound mixtures of which components are recognized by different chemoreceptors. Little information is available as to the key components in root exudates and their receptors that drive colonization related chemotaxis. We present here the first global assessment of this issue using the plant growth‐promoting rhizobacterium (PGPR) Bacillus velezensis SQR9 (formerly B. amyloliquefaciens). This strain efficiently colonizes cucumber roots, and here, we show that chemotaxis to cucumber root exudates was essential in this process. We conducted chemotaxis assays using cucumber root exudates at different concentrations, individual exudate components as well as recomposed exudates, taking into account their concentrations detected in root exudates. Results indicated that two key chemoreceptors, McpA and McpC, were essential for root exudate chemotaxis and root colonization. Both receptors possess a broad ligand range and recognize most of the exudate key components identified (malic, fumaric, gluconic and glyceric acids, Lys, Ser, Ala and mannose). The remaining six chemoreceptors did not contribute to exudate chemotaxis. This study provides novel insight into the evolution of the chemotaxis system in rhizobacteria. [ABSTRACT FROM AUTHOR]

Abstract Fusarium wilt disease of banana, caused by the fungus Fusarium oxysporum f. sp. cubense race 4, is a serious soil-borne fungal disease that currently threatens worldwide banana production. No single agricultural practice has yet been developed to effectively manage this disease. In the present study, greenhouse experiments were conducted to evaluate the effect of an integrated biofertilizer application after ammonia fumigation to enhance control of Fusarium wilt disease in severely infected banana mono-cropped soils. Quantitative PCR and high-throughput sequencing were used to characterise soil microbial community structure and the results from both two-season experimental studies showed that biofertilizer application after ammonia fumigation significantly reduced the incidence of banana Panama disease by approximately 55% and promoted the plant biomass, compared to the control application of cow manure to non-fumigated soil. Ammonia fumigation significantly reduced total fungal and F. oxysporum abundances and bacterial and fungal diversities. Biofertilizer application after fumigation further depleted the abundance of the pathogen. Biofertilizer application and fumigation altered the soil microbial community composition with the bacterial community responding first to fumigation, while the fungal community responded first to fertilization. Although Bacillus , including our inoculated strain, was not enriched after biofertilization, putative beneficial microbes such as Paenibacillus , Virgibacillus , Nitrosomonas , and Nitrobacter , were significantly enriched by ammonia fumigation and biofertilizer application, and were significantly correlated with disease suppression or increased plant biomass. Furthermore, fumigation and biofertilization significantly increased the soil pH and nutrient contents, with concomitant effects on the microbial community. Overall, the observed disease suppression and increased plant biomass resulting from both soil fumigation and biofertilization after banana cropping can be attributed to the reduced abundance of F. oxysporum and general suppression from altered soil properties that may enable the establishment of a beneficial soil microbiome. Highlights • Integrated biofertilizer application and fumigation enhanced Fusarium wilt disease suppression. • Ammonia fumigation significantly reduced F. oxysporum abundance. • Biofertilizer application after fumigation further depleted the abundance of the pathogen. • An increase in the number of known beneficial microbes is correlated with disease suppression. [ABSTRACT FROM AUTHOR]

The effect of genetic markers and reference databases on analyses of fungal communities were estimated using fungal large subunit (LSU) and internal transcribed spacer (ITS) amplicon datasets in consecutive years of rhizosphere samples from three candidate biofuel crops, corn (Zea mays), switchgrass (Panicum virgatum), and miscanthus (Miscanthus × giganteus). These two marker genes were selected to contrast possible differences in biological conclusions. In addition, two ITS schemes based on two ITS reference databases were used to assess differences due to reference database composition. A taxonomy-supervised method was invoked using the Ribosomal Database Project naïve Bayesian classifier that accesses all three databases. The UNITE classification scheme had the highest number of classified taxa in the raw classification result; however, it also had the highest proportion of unknown taxa (sequences that were classified to "unclassified," "unidentified," incertae sedis or, in the case of Warcup, to matches containing two unique names). After removal of these unknown taxa, LSU had the highest classification rate followed by Warcup and UNITE. As expected, the communities resolved using the two ITS databases, based on the same sequences, were relatively more similar than those from the lower-coverage LSU classification scheme. The choice of marker gene or even the same reads with different classification databases revealed different community patterns due to database coverage, e.g., the relative abundance of the most abundant groups changed or were only detected in one or two of the classification schemes, such as for Mortierella, Fusarium, and Phoma. No marked difference in fungal beta-diversity was identified among the three methods. Differentiation between the three biofuel crops and between the drought and normal rainfall years was apparent, regardless of method. Though classification rates, taxonomic conflicts, and coverage differences within the high-abundance fungal groups varied according to classification scheme, there was no overall impact on beta diversity among the three methods. [ABSTRACT FROM AUTHOR]

Plant growth-promoting rhizobacteria (PGPR) have been reported to influence plant growth, yield, and nutrient uptake by an array of mechanisms. Uncovering the behavioral dynamics of PGPR is one of the most important issues necessary for understanding their functional performances. In this study, strain NJAU-Z9 which was found to possess complex functions and efficient rhizospheric colonization ability was selected from plenty of bacterial strains isolated randomly from the pepper rhizosphere soil and identified as Bacillus velezensis. Repeated seedling nursing tests performed absolute growth-promoting advantage for the novel isolated strain. After that, primers for the quantitative detection were designed based on its whole genome sequence (WGS), and a real-time PCR method was utilized to explore strategies for monitoring the strain in natural soil and in the pepper rhizosphere. Results showed based on the whole genome, two primers were identified as NJAU-Z9-specific quantitative PCR primers. Two seasonal pot experiments demonstrated that strain NJAU-Z9 effectively colonized the rhizosphere measured by the novel abundance detecting strategy, improved plant growth, and showed a positive correlation between bacterial number and biomass. This study offers a strategy based on a real-time PCR method for directly monitoring B. velezensis strain NJAU-Z9 in the soil and the rhizosphere and provides a reference for the quantitative study of other PGPR strains based on WGSs. [ABSTRACT FROM AUTHOR]

Transgenic Bacillus thuringiensis (Bt) rice extends significant protection against insect pests and meets the increasing demands for food and energy. Many studies have been conducted investigating the impacts of Bt rice to the agricultural ecosystem, but much less attention has been given to efforts attempting to determine how the presence of Bt rice influences and shapes the microbial community, especially the active microbes. Stable isotope probing and high-throughput sequencing were employed to explore the active microbes involved in Bt-containing straw decomposition. Compared to its near isoline, the Bt straw contained higher contents of total N, total P, total K, lignin, cellulose, and Cry1Ab toxin protein. These chemical differences did not affect the decomposition rate but significantly changed the active microbial decomposer communities. During the decomposition of Bt-containing straw, fungi were more affected than bacteria. Agromyces, Terrabacter, Microbacterium, Glycomyces, and Kribbella were the most representative unique (existed only in the Bt treatments and appeared at the early stage) bacterial genera, and Trichoderma was the most representative unique fungal genus in the Bt straw decomposition. By using similarity index calculation and function prediction, the significant differences between Bt straw and non-Bt straw treatments were found to be transient for both microbial taxa and functional traits. These results suggested that Bt rice has a significant but transient impact on soil microbes in terms of microbial straw decomposition. [ABSTRACT FROM AUTHOR]

Abstract Non-ribosomal peptides (NRPs) are one of the largest groups of natural microbial secondary metabolites, which include peptides such as the antibiotics vancomycin and gramicidin, as well as lipopeptides (surfactin, iturin A and bacillomycin). In this study, banana Fusarium wilt disease suppressive and conducive soils were chosen to investigate the role of microbes that harbor the NRPS gene in disease suppression based on the 454-pyrosequencing platform and real-time PCR technique. The results showed that higher abundances and diversity of microbes that harbor the NRPS gene were observed in the suppressive soil samples than in the conducive soil. According to the results of the DNA sequences blastx of NRPS, the main microbial taxa harboring the NRPS gene were identified, and Pseudomonas in Proteobacteria and Streptomyces in Actinobacteria might be remarkably related to Fusarium wilt disease suppression. Furthermore, the Mantel test showed that compared with bacteria community and chemical properties, the microbial community harboring the NRPS gene had a more significant impact on the disease incidences of Fusarium wilt. This study provided non-specific relationships between groups of microbes harboring NRPS genes and Fusarium wilt disease suppression suggesting potential interaction based on correlation evidence, and pointed out a potential mechanism of suppressive soil. [ABSTRACT FROM AUTHOR]

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p < 0.05) increased the soil pH and content of soil total C and available P and K, and this probably reshaped soil microbial community as revealed by redundancy analysis and variance partitioning analysis. The observed disease suppression due to biofertilizer application after soil fumigation can be attributed to the reduced abundance of F. oxysporum by general suppression resulting from manipulated soil properties and recovered soil microbiome. [ABSTRACT FROM AUTHOR]

Bacillus amyloliquefaciens NJN-6, a plant growth promoting bacterium can act as an efficient antagonist against F. oxysporum f. sp. cubense (FOC). This study tests the response of antibiotic producing genes ( itu A and bam D) and biofilm formation related genes ( eps D and yqx M) in strain NJN-6 to phenolic acids in banana root exudates. Phenolic acid in banana root exudates (infected or non-infected by FOC) were identified by HPLC. Transcription analysis of genes involved in biofilm formation and antibiotic synthesis in strain NJN-6 were investigated with quantitative reverse transcription PCR (RT-qPCR). We found that the transcription levels of two antibiotic producing genes and two biofilm formation related genes in strain NJN-6 were upregulated in the banana seedling roots. Root secretion of phthalic acid, salicylic acid and cinnamic acid were enhanced in FOC infected banana seedlings. Further additional experiments demonstrated that the transcription level of itu A, bam D and eps D increased linearly to the concentration of phthalic acid. Results from antibiotic production and biofilm formation assays demonstrated a similar trend to gene transcription analysis. The results in this study indicated that the phenolic acids in root exudates of banana can potentially enhance root colonization and pathogen suppression abilities of Bacillus amyloliquefaciens NJN-6. [ABSTRACT FROM AUTHOR]

Nitric oxide (NO) is an important gas signal that regulates many biological processes, and due to the high nitrogen recycling activity in the rhizosphere, NO is an important signaling molecule in this region. Thus, an understanding of the effect of NO on the rhizomicrobiome, especially on plant beneficial rhizobacteria, is important for the use of these bacteria in agriculture. In this study, the effect of exogenous NO on the beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 was investigated. The results showed that low concentrations of NO increased the ability of the strain SQR9 to form biofilms, while high concentrations of NO inhibited the growth of this bacterium. The SQR9 gene yflM encodes nitric oxide synthase (NOS), which is used to synthesize NO, while the gene ykvO encodes a sepiapterin reductase that is used to synthesize tetrahydrobiopterin, the coenzyme of NOS. Isothermal titration calorimetry and high-performance liquid chromatography analyses demonstrated an interaction between YkvO and NADPH. SQR9 has two hmp genes, although only one was observed to be responsible for NO detoxification through oxidization. This study revealed the effect of NO on plant beneficial rhizobacterium and assessed the ability of this strain to adapt to exogenous NO, which will help to improve the application of this strain in agricultural production. [ABSTRACT FROM AUTHOR]

Redox-associated events are important in plant development and responses to environmental stresses. In this study, we investigated spatial redox responses of cucumber ( Cucumis sativus L.) leaves to biotic stress ( Fusarium infection) or abiotic stress (water stress). Plants were grown under hydroponic conditions and either treated with polyethylene glycol to simulate drought or infected with Fusarium oxysporum f. sp. cucumerinum. Both water stress and Fusarium infection restricted cucumber growth and were associated with cellular plasma-membrane damage, reactive oxygen species accumulation, and changes in antioxidants; however, the responses to each stress were distinctive. Under water stress, H 2 O 2 generation at the leaf edge increased 29.7% compared with that at the centre but with Fusarium infection there was a relative 10.4% decrease at the edge. These changes correlated with changes in antioxidants and linked enzyme activities. The key sources of variation in oxidative events were defined by principal component analysis of all of the data and redox balance evaluations. We suggest that these spatial differences under water stress and Fusarium infection arise from discrete regulatory mechanisms, reflecting either developmental effect over the leaf regions or systemic anti-oxidative events occurred following infection. [ABSTRACT FROM AUTHOR]

Although numerous studies suggest that organic amendments are better at maintaining soil fertility and crop production than mineral-only fertilization, it is unclear if this occurs in different agricultural systems on a global scale. Here we report a comprehensive meta-analysis of 690 independent experiments comparing the performance of organic amendments and mineral-only fertilization on crop yields, the soil organic carbon (SOC) and total nitrogen (TN) contents, soil nutrient dynamics and biological properties. Our analysis shows that organic amendments increased crop yields on average of 27% than mineral-only fertilization. Farmyard manure (FYM) had the highest effect (49% increase) and this was especially clear in wheat croplands (40% increase). Organic amendment increased the amount of SOC (38%), TN (20%), microbial biomass carbon (MBC; 51%) and microbial biomass nitrogen (MBN; 24%) than mineral-only fertilization. Organic amendments also increased the soil microbiome enzyme activity in terms of soil hydrolytic C acquisition (C-acq; 39%), N acquisition (N-acq; 22%), P acquisition (P-acq; 48%) and oxidative decomposition (OX; 58%). Increased nutrient acquisition and oxidative decomposition could explain the positive effects of organic amendment on crop yields. These observed patterns were consistent for most organic amendments and cropping systems in diverse regions of the world. In summary, our analysis suggests that organic amendments can improve microbe-mediated soil ecosystem functioning, long-term soil fertility and crop productivity, relative to mineral fertilization, on a global scale. [ABSTRACT FROM AUTHOR]

Fungal communities may have different response to fertilization under different conditions. Therefore, it is necessary to reveal the effects of fertilizations on fungal communities considering temporal heterogeneity at different crop stages. To address this, soil samples were collected across eight typical plant growth stages of a wheat-rice rotation system under four fertilization regimes: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and organic fertilizer (OF). Soil temperature and moisture that co-vary with plant growth stages were the strongest predictors of fungal community compositions; meanwhile, fertilization regimes also played important roles. Shannon index and the relative abundance of Ascomycota were consistently increased when compared OF treatment with CF and OIMF treatments, while CF treatment had a higher relative abundance of Zygomycota when compared with NNF and OF treatments. For the functional guilds, application of urea-nitrogen fertilizers (CF and OIMF treatments) significantly decreased the relative abundance of saprotrophs and symbiotrophs, while soil treated with OF had less relative abundance of pathotrophs when compared to inorganic fertilizers. Our study provided a detailed picture of how fungal community composition responded to fertilization regimes across different plant growth stages. [ABSTRACT FROM AUTHOR]

Research into plastic-degrading bacteria and fungi is important for understanding how microorganisms can be used to address the problem of plastic pollution and for developing new approaches to sustainable waste management and bioplastic production. In the present study, we isolated 55 bacterial and 184 fungal strains degrading polycaprolactone (PCL) in plastic waste samples from Dafeng coastal salt marshes, Jiangsu, China. Of these, Jonesia and Streptomyces bacteria also showed potential to degrade other types of petroleum-based polymers. The metabarcoding results proved the existence of plastisphere as a distinct ecological niche regardless of the plastic types where 27 bacterial and 29 fungal amplicon sequence variants (ASVs) were found to be significantly (p < 0.05) enriched, including some belonging to Alternaria (Ascomycota, Fungi) and Pseudomonas (Gammaproteobacteria, Bacteria) that were also mined out by the method of cultivation. Further assembly analyses demonstrated the importance of deterministic processes especially the environmental filtering effect of carbon content and pH on bacteria as well as the carbon and cation content on fungi in shaping the plastisphere communities in this ecosystem. Thus, the unique microbiome of the plastisphere in the terrestrial-marine ecotone is enriched with microorganisms that are potentially capable of utilizing petroleum-based polymers, making it a valuable resource for screening plastic biodegraders. [Display omitted] • Coastal plastic debris has a unique microbiome compared to surrounding soil. • Deterministic processes dominate the microbial assembly in plastisphere. • 55 bacteria and 184 fungi capable of degrading PCL were found. • Plant pathogenic fungi are more frequent in plastisphere compared to saprotrophs. • Jonesia spp. bacteria show potential as bioeffectors for plastic degradation. [ABSTRACT FROM AUTHOR]

Soil microorganisms play an essential role in the redistribution of soil aggregate sizes due to the microenvironmental changes. Yet, little is known regarding how individual microbial taxa within different-sized aggregates respond to agronomic practice. This study integrated physical, chemical, and molecular techniques (i.e., high-throughput DNA sequencing and qPCR) to assess the influence of corn-tobacco rotation on the soil microbial community at the soil microenvironment scale, i.e., within mega- (>2 mm), macro- (0.25–2 mm) and micro-aggregate (<0.25 mm) fractions. The soil samples (0–20 cm) analyzed in this study originated from corn and tobacco, which were cultivated under three different fertilization regimes. The results demonstrate that corn-tobacco rotation substantially impacted the distribution of aggregate sizes, and the shift in soil microbial communities associated with soil aggregates was related to changes in soil total carbon (TC), the C/N ratio and pH. The indicator microbial taxa (i.e., those were sensitive to crop rotation) varied with aggregate size. When compared with tobacco soil, the corn soil showed higher relative abundances of probably more copiotrophic taxa across large-sized aggregates, also with more bacteria in mega-aggregates and more fungi in macro-aggregates. Changes in total microbial communities associated with mega- and macro-aggregates in response to crop rotation were driven mainly by alterations in bacterial and fungal communities, respectively. Overall, the results of this study demonstrate that soil aggregate size strongly affected the microbial community composition on agricultural fields, promoting the differential responses between bacteria and fungi to crop rotation in specific size of aggregates. [ABSTRACT FROM AUTHOR]

Soil protists, critical components of the soil microbiome and useful bio-indicators for soil quality, are often overlooked in microbial ecology. Here, a long-term field experiment with a cucumber monoculture was adopted to disentangle the influence of Trichoderma- enriched bio-fertilizers (BF) and organic fertilizers (OF) on the soil protists compared with that of chemical fertilizers (CF) without extra microbial inoculation. The results showed CF application was associated with lower protist richness and diversity than applications of and BF in both bulk and rhizosphere soils. Principal coordinate analysis revealed significant differences in the bulk and rhizosphere soil protist community structures, and the structures from CF treatment were obviously distinct from those resulting from OF and BF treatments in both bulk and rhizosphere soils. Moreover, in bulk soils, OF had higher relative abundances of Alveolata, Amoebozoa, Archaeplastida and Opisthokonta than did CF and BF. Compared with rhizosphere soils, Alveolata and Amoebozoa increased in bulk soil with CF, while the latter group decreased with OF. The most abundant OTUs were assigned to functional groups, and it was found that omnivores were on average, but not significantly, more abundant in bulk soil compared to rhizospheres. OTU_144 ( Acanthamoebidae arachisporum ) increased while OTU_54 (Hypotrichia, belonging to omnivores) decreased from bulk to rhizosphere soils in all treatments. Overall, we conclude that soil management strategies such as organic amendments can greatly alter the bulk soil protist community and that plants can further select protist community in the rhizosphere with potential consequences for plant growth in agricultural systems. [ABSTRACT FROM AUTHOR]

Paddy soils constitute the largest anthropogenic wetlands on earth. However, the biogeochemical cycles of iron (Fe) oxides and organic compounds at the redox interfaces in paddy soils are poorly understood. Here, we propose a conceptual mechanism based on our data set, which links seasonal turnover of soil aggregates and the organo-mineral associations at the aggregate interfaces in the rice-wheat cropping system. Our results showed that the application of organic amendments significantly ( P  < 0.05) increased the aggregate mean weight diameter (MWD) compared to chemical fertilization alone. The aggregate MWD was always higher after the wheat harvest than after the rice harvest from 2013 to 2015, indicating a seasonal dynamic management-induced process of aggregation, disaggregation and re-aggregation. The oxalate-extractable Fe oxides (Feo) may preferentially retain aromatic organic compounds as indicated by the significant positive correlation between Feo and the percentage of aromatic carbon (C). Furthermore, the specific surface area of the ferrihydrite significantly increased after the microbial reduction, showing the potential of adsorbing more aromatic organic compounds. Moreover, there were more aromatic organic compounds at the aggregate surfaces than in the entire entities, suggesting that aromatic organic compounds were selectively preserved at the aggregate interfaces possibly by forming aromatic-Fe complexes. Therefore, soil disaggregation coupled with the anaerobic conditions exposed more fresh surfaces for C accumulation by forming aromatic-Fe complexes, which were subsequently protected by soil re-aggregation in the aerobic conditions. Organic fertilization improved soil aggregation and promoted the organo-mineral interactions, thus contributing to C sequestration in the rice-wheat cropping system. [ABSTRACT FROM AUTHOR]

Abstract: An increasing number of studies indicate that microbial diversity plays a crucial role in the mediation of ecosystem multifunctionality (EMF) in natural ecosystems. However, this point remains mostly overlooked in managed ecosystems, especially in agriculture. Here, we compiled promising strategies for the targeted exploitation of the associations between microbial diversity and EMF of agricultural soils using samples from two long‐term (more than 30 years) experimental field sites in southern China. The two sites experienced a similar monsoon climate and fertilization management practices. We used high‐throughput amplicon sequencing, structural equation modelling and random forest analysis, to analyse our data and validate our hypotheses. We found that soil physiochemical properties and the C‐, N‐, P‐ and S‐cycle enzyme activities were increased with the increase in microbial diversity. Specifically, a positive linear relationship was observed between microbial diversity and EMF, which was mediated by long‐term fertilization management via changes in soil microbial communities and physiochemical properties. Random forest analysis and SEM showed that the important role of microbial diversity on EMF was maintained even when simultaneously taking multiple multifunctionality drivers (soil physiochemical properties, soil aggregation and enzymatic patterns) into account. In addition, microbial diversity, C‐cycle enzyme activity and pH value are feasible predictors of EMF; these factors were shown to be the main drivers of EMF of arable soils. Our findings suggest that there may be a limited degree of multifunctional redundancy in arable soils. The relationship we observed between microbial diversity and EMF suggests that management practices that foster more diverse soil microbial communities may have the potential to improve the functioning of agroecosystems. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

In continuously cropped fields, residues from decomposing watermelon plants are a primary source of autotoxins, which can inhibit watermelon growth and facilitate invasion of soil-borne pathogens. The composition of the autotoxins produced and the primary microbial decomposers remain unknown. Therefore, a microcosm experiment was conducted to identify the produced volatile organic compounds (VOCs, majority of which are believed to act as autotoxins) as well as the bacteria decomposers of watermelon residue decomposition in Fusarium -infested soil at 7, 14, 30 and 45 days post-inoculation (dpi) by gas chromatography–mass spectrometry (GC–MS) and 13 C-DNA stable isotope probing-denaturing gradient gel electrophoresis ( 13 C-DNA-SIP-DGGE), respectively. Our results indicate that at the beginning of decomposition, there was an increase in the formation of complex phenolic, alcoholic and ester compounds (e.g., 2,6-Bis(1,1-dimethylethyl)-4-(1-oxopropyl)phenol), whereas at 45 dpi, the VOCs were alkenes and alkanes (e.g., dodecane, caryophyllene, pentadecane) with simple structures. The residue-C assimilating community was dominated by the Phyla Alphaproteobacteria , Betaproteobacteria and Firmicutes at 7 dpi. From 14 to 45 dpi, Gammaproteobacteria together with Alphaproteobacteria became dominant. In total, there were 27 bacterial species from 9 phyla that utilized the 13 C-residues in the microcosms. Although the VOC profiles and bacterial decomposers might vary from soils and conditions, these results increase our understanding of residue decomposition of autotoxins and may contribute to mitigate soil-borne disease via crop residue management in field practice. [ABSTRACT FROM AUTHOR]

The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria- to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soil-borne Fusarium wilt disease. [ABSTRACT FROM AUTHOR]

Bacillus velezensis strain SQR9 is a well-investigated rhizobacterium with an outstanding ability to colonize roots, enhance plant growth and suppress soil-borne diseases. The recognition that biofilm formation by plant-beneficial bacteria is crucial for their root colonization and function has resulted in increased interest in understanding molecular mechanisms related to biofilm formation. Here, we report that the gene ftsE , encoding the ATP-binding protein of an FtsEX ABC transporter, is required for efficient SQR9 biofilm formation. FtsEX has been reported to regulate the atolysin CwlO. We provided evidence that FtsEX-CwlO was involved in the regulation of SQR9 biofilm formation; however, this effect has little to do with CwlO autolysin activity. We propose that regulation of biofilm formation by CwlO was exerted through the spo0A pathway, since transcription of spo0A cascade genes was altered and their downstream extracellular matrix genes were downregulated in SQR9 ftsE/cwlO deletion mutants. CwlO was also shown to interact physically with KinB/KinD. CwlO may therefore interact with KinB/KinD to interfere with the spo0A pathway. This study revealed that FtsEX-CwlO plays a previously undiscovered regulatory role in biofilm formation by SQR9 that may enhance root colonization and plant-beneficial functions of SQR9 and other beneficial rhizobacteria as well. [ABSTRACT FROM AUTHOR]

Plant pathogen invasions are often associated with changes in physical environmental conditions and the composition of host-associated rhizosphere microbiome. It is however unclear how these factors interact and correlate with each other in determining plant disease dynamics in natural field conditions. To study this, we temporally sampled the rhizosphere of tomato plants that were exposed to moderate to aggressive Ralstonia solanacearum pathogen invasions over one crop season. We found that physiochemical soil properties correlated weakly with the severity of pathogen invasion apart from the water-soluble nitrogen concentration, which increased more clearly during the aggressive invasion. Instead, a much stronger link was found between pathogen invasion and reduced abundance and diversity of various rhizosphere bacterial taxa, simplification of bacterial interaction networks and loss of several predicted functional genes. We further verified our results in a separate greenhouse experiment to show that pathogen invasion causally drives similar changes in rhizosphere microbiome diversity and composition under controlled environmental conditions. Our results suggest that R. solanacearum invasion disrupts rhizosphere bacterial communities leading to clear reduction in the diversity and abundance of non-pathogenic bacteria. These changes could potentially affect the likelihood of secondary pathogen invasions during following crop seasons as less diverse microbial communities are also often less resistant to invasions. Strong negative correlation between pathogen and non-pathogenic bacterial densities further suggest that relative pathogen abundance could better predict the severity of bacterial wilt disease outbreaks compared to absolute pathogen abundance. Monitoring the dynamics of whole microbiomes could thus open new avenues for more accurate disease diagnostics in the future. [ABSTRACT FROM AUTHOR]

Background and aims: Considering the global demands in sustaining agriculture, use of organic amendments is gradually increasing. An improved understanding of the biological process is essential to evaluate the performance of organic amendments on agro-ecosystem.Methods: Soils subjected to different fertilization regimes were collected from a field experiment. Microbial community compositions are assessed with 16S and ITS rRNA gene sequencing and subsequent bioinformatics analysis. Microbial functions are characterized with the geometric mean of the assayed enzyme activities (GMea) and the microbial carbon-use efficiency:nitrogen-use efficiency ratio (CUE:NUE).Results: Compared with the chemically fertilized soil, the GMea significantly increased in organically amended soils. In contrast, the CUE:NUE was highest in chemically treated soil. These changes of microbial functional indicators were associated with shifts in the bacterial and not the fungal community composition, despite the fact that both the bacterial and fungal community compositions were significantly affected by the fertilization regimes. The abundances of specific soil bacterial taxa, especially the genera Luteimonas and Gemmatimona, were enriched by organic amendments. Soil organic carbon emerged as the major determinant of the bacterial community composition.Conclusions: Soil microbial activities and nutrient-use efficiencies were dramatically changed along with the alteration of bacterial community composition. Relatively greater abundance of Luteimonas and Gemmatimona taxa in soils might be useful indicators for soil amelioration. Our research could be helpful to provide better strategies for the maintenance of soil fertility. [ABSTRACT FROM AUTHOR]

Nitrogen is a macronutrient which plays an important role in the net primary productivity of terrestrial ecosystems, and is critical to understand how nitrogen addition affects above- and below-ground organisms. However, direct and indirect interactions between microbial species response to nitrogen addition for wheat growth are still unclear. In this study, arbuscular mycorrhizal fungi (AMF) and diazotrophs ( nifH gene) were selected as two groups of key functional microbes in wheat soil to investigate the comprehensive impact of diversity and community structures between them on wheat yield under a nitrogen gradient. Nitrogen addition resulted in a significant shift in AMF and nifH phylogenetic diversity and community structure. The interactions among AMF and nifH species were diminished in high N-treated soils compared to those in low N-treated soils. Structural equation model analysis showed that AMF community structure affected wheat yield directly, however, which was influenced by AMF diversity, diazotrophic diversity and community structure indirectly. The comprehensive effects of AMF and diazotrophs on wheat productivity indicated the importance of soil functional microbes as drivers for farmland ecosystem and plant growth. These results could be useful in understanding soil nutrient cycling and may help improve the mechanistic understanding of the tripartite interaction among nitrogen addition, microbes and wheat productivity. [ABSTRACT FROM AUTHOR]

Different fractions during the 85-day windrow composting were characterized based on various parameters, such as physiochemical properties and hydrolytic enzyme activities; several technologies were used, including spectral scanning techniques, confocal laser scanning microscopy (CLSM) and 13 C Nuclear Magnetic Resonance Spectroscopy ( 13 C NMR). The evaluated parameters fluctuated strongly during the first 3 weeks which was the most active period of the composting process. The principal components analysis (PCA) results showed that four classes of the samples were clearly distinguishable, in which the physiochemical parameters were similar, and that the dynamics of the composting process was significantly influenced by C/N and moisture content. The 13 C NMR results indicated that O-alkyl-C was the predominant group both in the solid and water-soluble fractions (WSF), and the decomposition of O-alkyl-C mainly occurred during the active stage. In general, the various parameters indicated that windrow composting is a feasible treatment that can be used for the resource reuse of agricultural wastes. [ABSTRACT FROM AUTHOR]

Although the precipitation and dissolution of iron (Fe)-containing-minerals are driven by microbially-mediated iron-redox cycling, we still have a limited understanding of complex response of such microbial communities to fertilisation. Here, using chemical and synchrotron-based spectral analyses, we show that the distribution of poorly crystalline Fe minerals and crystalline Fe minerals is different in organically- and inorganically-fertilised soils, and that compared to no fertilisation (Control), Fe redox cycling bacteria were present at higher abundance and diversity in organically-fertilised soils but lower in inorganically-fertilised soil. During Fe(III) reduction, Geobacter were important active Fe(III) reducers, with a higher relative abundance in both organically- and inorganically-fertilised soils than in Control, and their higher abundance was responsible for greater dissolution of ferrihydrite in inorganically-fertilised soil than in organically-fertilised soil. However, during the Fe(II) oxidation, Pseudomonas and Anaerolinea were more abundant, and produced higher levels of poorly crystalline Fe oxides under organic fertilisation. Thus, for the first time, we demonstrate that inorganic and organic fertilisation regimes have contrasting effects on the Fe redox bacterial communities, which then influence Fe cycling in soils. [ABSTRACT FROM AUTHOR]

Aims: Bio-organic fertilizer and different additives are widely applied to suppress soil-borne diseases. However, how different additives alter bulk soil microflora and thereby induce the healthy rhizospheric microflora remains unclear.Methods: A 3-season field experiment containing four fertilization management programs (chemical fertilizer, organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer was conducted in a tomato production agroecosystem with high disease incidence to evaluate the induced efficacy. The bacterial and fungal microflora of bulk and rhizosphere soil influenced by different management programs were performed on the Illumina MiSeq platform. Principal coordinate analysis based on the Bray-Curtis distance metric was performed to compare the similarities and differences of the bacterial and fungal community compositions among all soil samples.Results: Soil amended with organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer progressively and significantly suppressed tomato diseases in comparison with chemical fertilizer, and bio-organic fertilizer presented the best efficacy in all seasons. Interestingly, rhizospheric and bulk soil bacterial and fungal communities of the different fertilization management programs were separated from each other. Six bacterial and 10 fungal rhizospheric genera positively correlated with the same genera observed in bulk soil showing significant relationships with tomato disease incidence were observed, and functional strain SQR9 can be detected in the bulk and rhizosphere soils of bio-organic fertilizer treatments. Additionally, the redundancy analysis results showed the genera in treated chemical fertilizer bulk soil were dominated by Ralstonia and Fusarium, the abundances of which were highest and lowest in treated chemical fertilizer and bio-organic fertilizer rhizosphere, respectively.Conclusions: This study provided insights into soil-borne disease suppression by bulk soil management and confirmed that alterations to the bulk soil microbiota by different organic additives played distinct roles in the formation of rhizospheric soil microflora for the suppression of disease. [ABSTRACT FROM AUTHOR]

Arsenic (As) biomethylation is an important component of the As biogeochemical cycle that can influence As toxicity and mobility in the environment. Biomethylation of As is catalyzed by the enzyme arsenite (As[III]) S-adenosylmethionine methyltransferase (ArsM). To date, all identified ArsM orthologs with As(III) methylation activities have four conserved cysteine residues, which are thought to be essential for As(III) methylation. Here, we isolated an As(III)-methylating bacterium, Bacillus sp. CX-1, and identified a gene encoding a S-adenosylmethionine methyltranserase termed BlArsM with low sequence similarities (≤ 39%) to other ArsMs. BlArsM has six cysteine residues (Cys10, Cys11, Cys145, Cys193, Cys195 and Cys268), three of which (Cys10, Cys145 and Cys195) align with conserved cysteine residues found in most ArsMs. BlarsM is constitutively expressed in Bacillus sp. CX-1. Heterologous expression of BlarsM conferred As(III) resistance. Purified BlArsM methylated both As(III) and methylarsenite (MAs[III]), with a final product of dimethylarsenate (DMAs[V]). When all six cysteines were individually altered to serine residues, only C145S and C195S derivatives lost the ability to methylate As(III) and MAs(III). The derivative C10S/C11S/C193S/C268S was still active. These results suggest that BlArsM is a novel As(III) S-adenosylmethionine methyltransferase requiring only two conserved cysteine residues. A model of As(III) methylation by BlArsM is proposed. [ABSTRACT FROM AUTHOR]

The photosynthetic rate increases under high-N supply, resulting in a large CO2 transport conductance in mesophyll cells. It is less known that water movement is affected by nitrogen supply in leaves. This study investigated whether the expression of aquaporin and water transport were affected by low-N (0.7 mM) and high-N (7 mM) concentrations in the hydroponic culture of four rice varieties: (1) Shanyou 63 (SY63), a hybrid variant of the indica species; (2) Yangdao 6 (YD6), a variant of indica species; (3) Zhendao 11 (ZD11), a hybrid variant of japonica species; and (4) Jiuyou 418 (JY418), another hybrid of the japonica species. Both the photosynthetic and transpiration rate were increased by the high-N supply in the four varieties. The expressions of aquaporins, plasma membrane intrinsic proteins (PIPs), and tonoplast membrane intrinsic protein (TIP) were higher in high-N than low-N leaves, except in SY63. Leaf hydraulic conductance (Kleaf) was lower in high-N than low-N leaves in SY63, while Kleaf increased under high-N supply in the YD6 variant. Negative correlations were observed between the expression of aquaporin and the transpiration rate in different varieties. Moreover, there was a significant negative correlation between transpiration rate and intercellular air space. In conclusion, the change in expression of aquaporins could affect Kleaf and transpiration. A feedback effect of transpiration would regulate aquaporin expression. The present results imply a coordination of gas exchange with leaf hydraulic conductance. [ABSTRACT FROM AUTHOR]

Aquaporins (AQPs) are integral membrane proteins facilitating the transport of water and some small neutral molecules across cell membranes. In past years, much effort has been made to reveal the location of AQPs as well as their function in water transport, photosynthetic processes, and stress responses in higher plants. In the present review, we paid attention to the character of AQPs in determining carbon and nitrogen status. The role of AQPs during photosynthesis is characterized as its function in transporting water and CO2 across the membrane of chloroplast and thylakoid; recalculated results from published studies showed that over-expression of AQPs contributed to 25% and 50% increases in stomatal conductance (gs) and mesophyll conductance (gm), respectively. The nitrogen status in plants is regulated by AQPs through their effect on water flow as well as urea and NH4 + uptake, and the potential role of AQPs in alleviating ammonium toxicity is discussed. At the same time, root and/or shoot AQP expression is quite dependent on both N supply amounts and forms. Future research directions concerning the function of AQPs in regulating plant carbon and nitrogen status as well as C/N balance are also highlighted. [ABSTRACT FROM AUTHOR]

Even though organic fertilization is known to promote soil nitrogen cycling ( N -cycling), it is unclear how this effect is mediated. Here we studied the potential roles of soil physiochemical properties and soil particle-size fraction (PSF) in relation to the diversity and abundance of N -cycling-related prokaryotes by sampling field sites that had been subjected to either mineral or organic fertilization for over 30 years (two independent fields subjected to both fertilization treatments). We found that organic fertilization increased the 63–200 μm sized soil fraction and the abundance of various N -cycling-related prokaryotes including diazotrophs, ammonia-oxidizers and denitrifiers. Moreover, increase in the abundance of different N -cycling-related prokaryotes varied between different size fractions: the abundance of ammonia-oxidizers and nitrate-reducers was the highest in the 63–200 μm size fraction, while the abundance of diazotrophs, ammonifiers and denitrifiers was the highest in the 200–2000 μm, 2–63 μm and 0.1–2 μm size fractions, respectively. According to structural equation modelling (SEM), soil PSF, physiochemical properties and the community structure of N -cycling-related prokaryotes within different PSFs were associated with the abundance of N -cycling-related prokaryotes in non-fractionated bulk soils. In conclusion, these results suggest that organic, but not mineral, fertilization can support the abundance of N -cycling-related prokaryotes and that the strength of the effects depends on their association with specific particle-size fractions. [ABSTRACT FROM AUTHOR]