The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome

Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens

BACKGROUND

Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36 found to have beneficial traits including plant growth promotion and broad-spectrum antifungal activity towards taxonomically diverse plant pathogens. Understanding the genomes will assist in devising a bioformulation for crop protection while exploiting their beneficial functional roles.

RESULTS

Two potential firmicute species were isolated from pearl millet panicles. Morphological, biochemical, and molecular characterization revealed their identities as Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36. The seed priming assays revealed the ability of both species to enhance plant growth promotion and seedling vigour index. Invitro assays with PBs 12 and PBl 36 showed the antibiosis effect against taxonomically diverse plant pathogens (Magnaporthe grisea; Sclerotium rolfsii; Fusarium solani; Alternaria alternata; Ganoderma sp.) of crops and multipurpose tree species. The whole genome sequence analysis was performed to unveil the genetic potential of these bacteria for plant protection. The complete genomes of PBs 12 and PBl 36 consist of a single circular chromosome with a size of 4.02 and 4.33 Mb and 4,171 and 4,606 genes, with a G + C content of 43.68 and 45.83%, respectively. Comparative Average Nucleotide Identity (ANI) analysis revealed a close similarity of PBs 12 and PBl 36 with other beneficial strains of B. subtilis and B. paralicheniformis and found distant from B. altitudinis, B. amyloliquefaciens, and B. thuringiensis. Functional annotation revealed a majority of pathway classes of PBs 12 (30) and PBl 36 (29) involved in the biosynthesis of secondary metabolites, polyketides, and non-ribosomal peptides, followed by xenobiotic biodegradation and metabolism (21). Furthermore, 14 genomic regions of PBs 12 and 15 of PBl 36 associated with the synthesis of RiPP (Ribosomally synthesized and post-translationally modified peptides), terpenes, cyclic dipeptides (CDPs), type III polyketide synthases (T3PKSs), sactipeptides, lanthipeptides, siderophores, NRPS (Non-Ribosomal Peptide Synthetase), NRP-metallophone, etc. It was discovered that these areas contain between 25,458 and 33,000 secondary metabolite-coding MiBiG clusters which code for a wide range of products, such as antibiotics. The PCR-based screening for the presence of antimicrobial peptide (cyclic lipopeptide) genes in PBs 12 and 36 confirmed their broad-spectrum antifungal potential with the presence of spoVG, bacA, and srfAA AMP genes, which encode antimicrobial compounds such as subtilin, bacylisin, and surfactin.

CONCLUSION

The combined in vitro studies and genome analysis highlighted the antifungal potential of pearl millet panicle-associated Bacillus subtilis PBs12 and Bacillus paralicheniformis PBl36. The genetic ability to synthesize several antimicrobial compounds indicated the industrial value of PBs 12 and PBl 36, which shed light on further studies to establish their action as a biostimulant for crop protection.

Bacillus velezensis WB induces systemic resistance in watermelon against Fusarium wilt

BACKGROUND

Our previous findings indicated that Bacillus velezensis WB could control Fusarium wilt by changing the structure of the microbial community in the watermelon rhizosphere. However, there are few studies on its mechanism in the pathogen resistance of watermelon. Therefore, in this study, we determined the mechanism of B. velezensis WB-induced systemic resistance in watermelon against Fusarium wilt through glasshouse pot experiments.

RESULTS

The results showed that B. velezensis WB significantly reduced the incidence and disease index of Fusarium wilt in watermelon. B. velezensis WB can enhance the basal immunity of watermelon plants by: increasing the activity of phenylalanine ammonia-lyase (PAL), peroxidase (POD), superoxide dismutase (SOD) and β-1,3-glucanase; accumulating lignin, salicylic acid (SA) and jasmonic acid (JA); reducing malondialdehyde (MDA) concentrations; and inducing callus deposition in watermelon plant cells. RNA-seq analysis showed that 846 watermelon genes were upregulated and 612 watermelon genes were downregulated in the WF treatment. This process led to the activation of watermelon genes associated with auxin, gibberellin, SA, ethylene and JA, and the expression of genes in the phenylalanine biosynthetic pathway was upregulated. In addition, transcription factors involved in plant resistance to pathogens, such as MYB, NAC and WRKY, were induced. Gene correlation analysis showed that Cla97C10G195840 and Cla97C02G049930 in the phenylalanine biosynthetic pathway, and Cla97C02G041360 and Cla97C10G197290 in the plant hormone signal transduction pathway showed strong correlations with other genes.

CONCLUSION

Our results indicated that B. velezensis WB is capable of inducing systemic resistance in watermelon against Fusarium wilt. © 2023 Society of Chemical Industry.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Manipulation of the seagrass-associated microbiome reduces disease severity

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.

Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture

Species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development. New mechanisms underlying Bacillus biocontrol activity have been revealed with the development of microbiome and microbe-plant interaction research. In this review, we first briefly introduce the typical Bacillus biocontrol mechanisms, such as the production of antimicrobial compounds, competition for niches/nutrients, and induction of systemic resistance. Then, we discussed in detail the new mechanisms of pathogen quorum sensing interference and reshaping of the soil microbiota. The "cry for help" mechanism was also introduced, in which plants can release specific signals under pathogen attack to recruit biocontrol Bacillus for root colonization against invasion. Finally, two emerging strategies for enhancing the biocontrol efficacy of Bacillus agents, including the construction of synthetic microbial consortia and the application of rhizosphere-derived prebiotics, were proposed.

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

Antifungal activity of cyclopaldic acid from Antarctic Penicillium against phytopathogenic fungi

Plant pathogens cause great economic losses in agriculture. To reduce damage, chemical pesticides have been frequently used, but these compounds in addition to causing risks to the environment and health, its continuous use has given rise to resistant phytopathogens, threatening the efficiency of control methods. One alternative for such a problem is the use of natural products with high antifungal activity and low toxicity. Here, we present the production, isolation, and identification of cyclopaldic acid, a bioactive compound produced by Penicillium sp. CRM 1540, a fungal strain isolated from Antarctic marine sediment. The crude extract was fractionated by reversed-phase chromatography and yielded 40 fractions, from which fraction F17 was selected. We used 1D and 2D Nuclear Magnetic Resonance analysis in DMSO-d6 and CDCl3, together with mass spectrometry, to identify the compound as cyclopaldic acid C11H10O6 (238 Da). The pure compound was evaluated for antimicrobial activity against phytopathogenic fungi of global agricultural importance, namely: Macrophomina phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. The antifungal assay revealed the potential of cyclopaldic acid, produced by Penicillium sp. CRM 1540, as a leading molecule against M. phaseolina and R. solani, with more than 90% of growth inhibition after 96h of contact with the fungal cells using 100 µg mL-1, and more than 70% using 50 µg mL-1.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03792-9.

Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis Q-426

BACKGROUND

The Q-426 strain isolated from compost samples has excellent antifungal activities against a variety of plant pathogens. However, the complete genome of Q-426 is still unclear, which limits the potential application of Q-426.

RESULTS

Genome sequencing revealed that Q-426 contains a single circular chromosome 4,086,827 bp in length, with 4691 coding sequences and an average GC content of 46.3%. The Q-426 strain has a high degree of collinearity with B. velezensis FZB42, B. velezensis SQR9, and B. amyloliquefaciens DSM7, and the strain was reidentified as B. velezensis Q-426 based on the homology analysis results. Many genes in the Q-426 genome have plant growth-promoting activity, including the secondary metabolites of lipopeptides. Genome mining revealed 14 clusters and 732 genes encoding secondary metabolites with predicted functions, including the surfactin, iturin, and fengycin families. In addition, twelve lipopeptides (surfactin, iturin and fengycin) were successfully detected from the fermentation broth of B. velezensis Q-426 by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS/MS), which is consistent with the genome analysis results. We found that Q-426 produced indole-3-acetic acid (IAA) at 1.56 mg/l on the third day of incubation, which might promote the growth of plants. Moreover, we identified eighteen volatile compounds (VOCs, including 2-heptanone, 6-methylheptan-2-one, 5-methylheptan-2-one, 2-nonanone, 2-decanone, 2-undecanone, 2-dodecanone, 2-tridecanone, 2-tetradecanone, 2-nonadecanone, pentadecanoic acid, oleic acid, dethyl phthalate, dibutyl phthalate, methyl (9E,12E)-octadeca-9,12-dienoate), pentadecane, (6E,10E)-1,2,3,4,4a,5,8,9,12,12a-decahydro-1,4-methanobenzo[10]annulene, and nonanal) based on gas chromatograph-mass spectrometer (GC/MS) results.

CONCLUSIONS

We mined secondary metabolite-related genes from the genome based on whole-genome sequence results. Our study laid the theoretical foundation for the development of secondary metabolites and the application of B. velezensis Q-426. Our findings provide insights into the genetic characteristics responsible for the bioactivities and potential application of B. velezensis Q-426 as a plant growth-promoting strain in ecological agriculture.

Bacillus subtilis ER-08, a multifunctional plant growth-promoting rhizobacterium, promotes the growth of fenugreek (Trigonella foenum-graecum L.) plants under salt and drought stress

Introduction

Sustainable agriculture and meeting the world's food needs face considerable obstacles from abiotic stresses such as soil salinity and drought. This critical issue was addressed by our current study, which sought to uncover multi-trait bioinoculants from hostile ecosystems that could help mitigate salinity and drought stresses at the same time.

Methods

The Bacillus subtilis ER-08 (BST) strain was isolated from the halotolerant plant Fagonia cretica which was collected from the Little Rann of Kachchh, India. Various biochemical and molecular approaches were applied for the detailed characterization of the BST isolate.

Results and discussion

The BST isolate demonstrated notable plant growth-promoting qualities. Fenugreek seed biopriming was performed using the BST isolate. The effect of BST seed treatment on fenugreek developmental indices as well as abiotic alleviation was examined under greenhouse conditions. The BST produced 83.7 g ml-1 gibberellins (GA3) and 176.1 g ml-1 indole-3 acetic acid. Moreover, hydrogen cyanide, siderophore, exopolysaccharides (EPS), ammonia, cellulase, protease, pectinase, and chitinase were also produced by the BST strain. Interestingly, 52% of Fusarium oxysporum mycelial growth was suppressed by the BST isolate under in vitro conditions. Furthermore, BST isolates functioned well under several abiotic stress conditions, for instance, salinity (4 and 6 ds m-1), pH (5, 7, and 9), drought (PEG6000 at 10%, 20%, and 30%), and temperature (25°C, 35°C, 37°C, and 55°C). This study indicates that the BST strain might serve as an effective bio-inoculant for minimizing the detrimental effects of abiotic stresses.

Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure

Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.

Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.

Plant microbiota dysbiosis and the Anna Karenina Principle

Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.

Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.

Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen, Fusarium oxysporum f. sp. vasinfectum (FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings. This article is protected by copyright. All rights reserved.

Bacillus velezensis SYL-3 suppresses Alternaria alternata and tobacco mosaic virus infecting Nicotiana tabacum by regulating the phyllosphere microbial community

The occurrence of plant diseases is closely associated with the imbalance of plant tissue microecological environment. The regulation of the phyllosphere microbial communities has become a new and alternative approach to the biological control of foliar diseases. In this study, Bacillus velezensis SYL-3 isolated from Luzhou exhibited an effective inhibitory effect against Alternaria alternata and tobacco mosaic virus (TMV). The analysis of phyllosphere microbiome by PacBio sequencing indicated that SYL-3 treatment significantly altered fungal and bacterial communities on the leaves of Nicotiana tabacum plants and reduced the disease index caused by A. alternata and TMV. Specifically, the abundance of P. seudomo, Sphingomonas, Massilia, and Cladosporium in the SYL-3 treatment group increased by 19.00, 9.49, 3.34, and 12.29%, respectively, while the abundances of Pantoea, Enterobacter, Sampaiozyma, and Rachicladosporium were reduced. Moreover, the abundance of beneficial bacteria, such as Pseudomonas and Sphingomonas, was negatively correlated with the disease indexes of A. alternata and TMV. The PICRUSt data also predicted the composition of functional genes, with significant differences being apparent between SYL-3 and the control treatment group. Further functional analysis of the microbiome also showed that SYL-3 may induce host disease resistance by motivating host defense-related pathways. These results collectively indicate that SYL-3 may suppress disease progression caused by A. alternata or TMV by improving the microbial community composition on tobacco leaves.

Exploring the Potential Applications of Paecilomyceslilacinus 112

Microorganisms are widely used to obtain biostimulants that can facilitate the assimilation of nutrients, ensuring high crop yield and quality. A particular category of biostimulants are protein hydrolyzates (PH), obtained from microbial cultures grown on a nutrient medium. In the present study, Paecilomyces lilacinus 112, an endophytic fungus isolated from soil, was tested to determine its effect on the growth promotion of tomato seedlings in greenhouse conditions. Additionally, other beneficial features of the P.lilacinus isolate were evaluated via several tests: antagonism against plant pathogenic fungi, production of secondary useful metabolites, and solubilization of vital micronutrients. Out of the tested pathogens, P.lilacinus exhibited the highest antifungal activity against a Cladosporium isolate (inhibition of 66.3%), followed by Rhizoctonia. solani (52.53%), and Sclerotinia sclerotiorum (50.23%). Paecilomyceslilacinus 112 was able to secrete hydrolytic enzymes and siderophores, and solubilize zinc and phosphorus. In the tomato treatment, the application of PH obtained from fungal cultivation on a feather medium led to the following increases in plant growth parameters: 3.54-fold in plant biomass; 3.26-fold in plant height, 1.28-fold in plant diameter; 1.5-fold in the number of branches/plant; and 1.43-fold in the number of leaves/plant, as compared to water treatment. The application of this isolate can be of benefit to bioeconomy because keratin wastes are valorized and returned, in agriculture, contributing to renewable natural resources.

Harnessing the microbiome to prevent global biodiversity loss

Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism

Background

Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed.

Results

In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified.

Conclusions

This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08330-0.

Major Biological Control Strategies for Plant Pathogens

Food security has become a major concern worldwide in recent years due to ever increasing population. Providing food for the growing billions without disturbing environmental balance is incessantly required in the current scenario. In view of this, sustainable modes of agricultural practices offer better promise and hence are gaining prominence recently. Moreover, these methods have taken precedence currently over chemical-based methods of pest restriction and pathogen control. Adoption of Biological Control is one such crucial technique that is currently in the forefront. Over a period of time, various biocontrol strategies have been experimented with and some have exhibited great success and promise. This review highlights the different methods of plant-pathogen control, types of plant pathogens, their modus operandi and various biocontrol approaches employing a range of microorganisms and their byproducts. The study lays emphasis on the use of upcoming methodologies like microbiome management and engineering, phage cocktails, genetically modified biocontrol agents and microbial volatilome as available strategies to sustainable agricultural practices. More importantly, a critical analysis of the various methods enumerated in the paper indicates the need to amalgamate these techniques in order to improve the degree of biocontrol offered by them.

Use of aqueous ozone rinsing to improve the disinfection efficacy and shorten the processing time of ultrasound-assisted washing of fresh produce

In minimal processing industry, chlorine is widely used in the disinfection process and ultrasound (US) increases the disinfection efficacy of chlorine and reduces the cross-contamination incidence during washing. Tap water (TW), which has no disinfection effect, is generally used to rinse off sanitizer residues on the surface of disinfected fresh-cut vegetables. In this study, aqueous ozone (AO), a low-cost and residue-free sanitizer, was used to replace TW rinsing in combination with US (28 kHz)-chlorine (free chlorine [FC] at 10 ppm, a concentration recommended for industrial use) for the disinfection of fresh-cut lettuce as a model. US-chlorine (40 s) + 2.0 ppm AO (60 s) treatment resulted in browning spots on lettuce surface at the end of storage. In contrast, US-chlorine (40 s) + 1.0 ppm AO (60 s) did not lead to deterioration of the sensory quality (sensory crispness, color, and flavor) and a change in total color difference, and the activities of browning-related enzymes were significantly lower. Moreover, US-chlorine (40 s) + 1.0 ppm of AO (60 s) treatment led to significantly lower counts of Escherichia coli O157:H7, Salmonella Typhimurium, aerobic mesophilic (AMC), and molds and yeasts (M&Y) on days 0-7 than US-chlorine (60 s) + TW (60 s) and single 1.0 ppm AO (120 s) treatments, suggesting that AO provided an additional disinfection effect over TW, while reducing the overall processing time by 20 s. Cell membrane permeability analysis (alkaline phosphatase, protein, nucleotide, and adenosine triphosphate leakage) showed that the combination with 1.0 ppm AO caused more severe cell membrane damage in E. coli O157:H7 and S. Typhimurium, explaining the higher disinfection efficacy. 16S rRNA sequencing revealed that following US-chlorine (40 s) + 1.0 ppm of AO (60 s) treatment, Massilia and Acinetobacter had higher relative abundances (RAs) on day 7 than after US-chlorine (60 s) + TW (60 s) treatment, whereas the RAs of Escherichia-Shigella was significantly lower, indicating that the former treatment has a superior capacity in maintaining a stable microbial composition. This explains from an ecological point of view why US-chlorine (40 s) + 1.0 ppm of AO (60 s) led to the lowest AMC and M&Y counts during storage. The study results provide evidence that AO has potential as an alternative to TW rinsing to increase the disinfection efficacy of US-chlorine.

Unlocking the Changes of Phyllosphere Fungal Communities of Fishscale Bamboo (Phyllachora heterocladae) under Rhombic-Spot Disease Stressed Conditions

As an important nonwood bioresource, fishscale bamboo (Phyllachora heterocladae Oliver) is widely distributed in the subtropical region of China. Rhombic-spot disease, caused by Neostagonosporella sichuanensis, is one of the most serious diseases that threatens fishscale bamboo health. However, there is limited knowledge about how rhombic-spot disease influences the diversity and structures of phyllosphere fungal communities. In this study, we investigated the phyllosphere fungal communities from stems, branches, and leaves of fishscale bamboo during a rhombic-spot disease outbreak using 18S rRNA sequencing. We found that only the phyllosphere fungal community from stems was significantly affected by pathogen invasion in terms of community richness, diversity, and structure. FUNGuild analysis revealed that the major classifications of phyllosphere fungi based on trophic modes in stems, branches, and leaves changed from symbiotroph-pathotroph, no obvious dominant trophic mode, and symbiotroph to saprotroph, saprotroph–pathotroph–symbiotroph, and saprotroph–symbiotroph, respectively, after pathogen invasion. The fungal community composition of the three tissues displayed significant differences at the genus level between healthy and diseased plants. The associations among fungal species in diseased samples showed more complex co-occurrence network structures than those of healthy samples. Taken together, our results highlight the importance of plant pathological conditions for the assembly of phyllosphere fungal communities in different tissues.

OUP accepted manuscript

During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.

Shifting Perspectives of Translational Research in Bio-Bactericides: Reviewing the Bacillus amyloliquefaciens Paradigm

Simple Summary

The continuous reduction of approved conventional microbicides, due to health concerns and the development of plant-pathogen resistance, has been urged for the use of safe alternatives in crop protection. Several beneficial bacterial species, termed biological control agents, are currently used in lieu of chemical pesticides. The approach to select such bacterial species and manufacture commercial products has been based on their biocontrol effect under optimal growth conditions, which is far from the real nutrient-limited field conditions of plant niches. It’s important to determine the complex interactions that occur among BCAs, plant host and niche microbiome to fully understand and exploit the potential of biological control agents. Furthermore, it’s crucial to acknowledge the environmental impact of their long-term use.

Abstract

Bacterial biological control agents (BCAs) have been increasingly used against plant diseases. The traditional approach to manufacturing such commercial products was based on the selection of bacterial species able to produce secondary metabolites that inhibit mainly fungal growth in optimal media. Such species are required to be massively produced and sustain long-term self-storage. The endpoint of this pipeline is large-scale field tests in which BCAs are handled as any other pesticide. Despite recent knowledge of the importance of BCA-host-microbiome interactions to trigger plant defenses and allow colonization, holistic approaches to maximize their potential are still in their infancy. There is a gap in scientific knowledge between experiments in controlled conditions for optimal BCA and pathogen growth and the nutrient-limited field conditions in which they face niche microbiota competition. Moreover, BCAs are considered to be safe by competent authorities and the public, with no side effects to the environment; the OneHealth impact of their application is understudied. This review summarizes the state of the art in BCA research and how current knowledge and new biotechnological tools have impacted BCA development and application. Future challenges, such as their combinational use and ability to ameliorate plant stress are also discussed. Addressing such challenges would establish their long-term use as centerfold agricultural pesticides and plant growth promoters.

Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter?

BACKGROUND

Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli.

RESULT

E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment.

CONCLUSION

Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

Effect of Direct Viral-Bacterial Interactions on the Removal of Norovirus From Lettuce

Norovirus (NoV) is the main non-bacterial pathogen causing outbreaks of gastroenteritis and is considered to be the leading cause of foodborne illness. This study aims to determine whether lettuce-encapsulated bacteria can express histo-blood group antigen (HBGA)–like substances to bind to NoV and, if so, to explore its role in protecting NoV from disinfection practices. Fifteen bacterial strains (HBGA-SEBs) were isolated from the lettuce microbiome and studied as they were proved to have the ability to express HBGA-like substances through indirect ELISA detection. By using attachment assay, HBGA-SEBs showed great abilities in carrying NoVs regarding the evaluation of binding capacity, especially for the top four strains from genera Wautersiella, Sphingobacterium, and Brachybacterium, which could absorb more than 60% of free-flowing NoVs. Meanwhile, the direct viral–bacterial binding between HBGA-like substance-expressing bacteria (HBGA-SEB) and NoVs was observed by TEM. Subsequently, results of simulated environmental experiments showed that the binding of NoVs with HBGA-SEBs did have detrimental effects on NoV reduction, which were evident in short-time high-temperature treatment (90°C) and UV exposure. Finally, by considering the relative abundance of homologous microorganisms of HBGA-SEBs in the lettuce microbiome (ca. 36.49%) and the reduction of NoVs in the simulated environments, we suggested putting extra attention on the daily disinfection of foodborne-pathogen carriers to overcome the detrimental effects of direct viral–bacterial interactions on the reduction of NoVs.

Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing

Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.

Genetic transformation system for Bacillus velezensis NSZ-YBGJ001 and curing of the endogenous plasmid pBV01

OBJECTIVES

To construct a genetic transformation system for Bacillus velezensis NSZ-YBGJ001 and identify the origin element in an endogenous plasmidpBV01 for curing pBV01 by plasmid incompatibility.

RESULTS

A plasmid pUBC01 was constructed, and then an electrotransformation system for B. velezensis NSZ-YBGJ001 was developed, which reached ~ 1000 transformants per microgram of pUBC01 DNA. Additionally, a 7276-bp circular plasmid pBV01 with a G + C content of 37.5% was isolated from B. velezensis NSZ-YBGJ001 and analyzed via sequence analysis. To cure pBV01, an incompatible plasmid pBV02 harboring the replication element of pBV01 was developed and functionally replicated in both Bacillus subtilis WB600 and B. velezensis NSZ-YBGJ001. pBV01 was cured through introduction of pBV02 into B. velezensis NSZ-YBGJ001 after serial subculturing for approximately 40 generations. Finally, another plasmid, pBV03, was constructed based on pBV-ori, and exogenous genes in pBV03 could be efficiently expressed in B. subtilis.

CONCLUSIONS

The results of this study, including the genetic transformation system, plasmid-curing strategy, and exogenous gene expression, will support genetic manipulation of B. velezensis to promote its application in biocontrol and industry.

Bioprospecting of Beneficial Bacteria Traits Associated With Tomato Root in Greenhouse Environment Reveals That Sampling Sites Impact More Than the Root Compartment

Tomato is subject to several diseases that affect both field- and greenhouse-grown crops. To select cost-effective potential biocontrol agents, we used laboratory throughput screening to identify bacterial strains with versatile characteristics suitable for multipurpose uses. The natural diversity of tomato root-associated bacterial communities was bioprospected under a real-world environment represented by an intensive tomato cultivation area characterized by extraseasonal productions in the greenhouse. Approximately 400 tomato root-associated bacterial isolates, in majority Gram-negative bacteria, were isolated from three compartments: the soil close to the root surface (rhizosphere, R), the root surface (rhizoplane, RP), and the root interior (endorhizosphere, E). A total of 33% of the isolates produced siderophores and were able to solubilize phosphates and grow on NA with 8% NaCl. A total of 30% of the root-associated bacteria showed antagonistic activity against all the tomato pathogens tested, i.e., Clavibacter michiganesis pv. michiganensis, Pseudomonas syringae pv. tomato, Pseudomonas corrugata and Xanthomonas euvesicatoria pv. perforans, and Fusarium oxysporum f. sp. lycopersici. We found that the sampling site rather than the root compartment of isolation influenced bacterial composition in terms of analyzed phenotype. This was demonstrated through a diversity analysis including general characteristics and PGPR traits, as well as biocontrol activity in vitro. Analysis of 16S rRNA gene (rDNA) sequencing of 77 culturable endophytic bacteria that shared multiple beneficial activity revealed a predominance of bacteria in Bacillales, Enterobacteriales, and Pseudomonadales. Their in vitro antagonistic activity showed that Bacillus species were significantly more active than the isolates in the other taxonomic group. In planta activity against phytopathogenic bacteria of a subset of Bacillus and Pseudomonas isolates was also assessed.

Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.

Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success

Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.

A Review on the Biotechnological Applications of the Operational Group Bacillus amyloliquefaciens

Bacteria under the operational group Bacillus amyloliquefaciens (OGBa) are all Gram-positive, endospore-forming, and rod-shaped. Taxonomically, the OGBa belongs to the Bacillus subtilis species complex, family Bacillaceae, class Bacilli, and phylum Firmicutes. To date, the OGBa comprises four bacterial species: Bacillus amyloliquefaciens, Bacillus siamensis, Bacillus velezensis and Bacillus nakamurai. They are widely distributed in various niches including soil, plants, food, and water. A resurgence in genome mining has caused an increased focus on the biotechnological applications of bacterial species belonging to the OGBa. The members of OGBa are known as plant growth-promoting bacteria (PGPB) due to their abilities to fix nitrogen, solubilize phosphate, and produce siderophore and phytohormones, as well as antimicrobial compounds. Moreover, they are also reported to produce various enzymes including α-amylase, protease, lipase, cellulase, xylanase, pectinase, aminotransferase, barnase, peroxidase, and laccase. Antimicrobial compounds that able to inhibit the growth of pathogens including non-ribosomal peptides and polyketides are also produced by these bacteria. Within the OGBa, various B. velezensis strains are promising for use as probiotics for animals and fishes. Genome mining has revealed the potential applications of members of OGBa for removing organophosphorus (OPs) pesticides. Thus, this review focused on the applicability of members of OGBa as plant growth promoters, biocontrol agents, probiotics, bioremediation agents, as well as producers of commercial enzymes and antibiotics. Here, the bioformulations and commercial products available based on these bacteria are also highlighted. This review will better facilitate understandings of members of OGBa and their biotechnological applications.

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables

Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.

Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity

Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

The contribution of surrounding plant microbiota to disease development has led to the 'pathobiome' concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defence-related genes (glucosinolate metabolism) in B. napus.

The endosphere bacteriome of diseased and healthy tomato plants

Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.

Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants

Nutrition-Sensitive Agriculture (NSA) is a novel concept in agriculture that considers not only yield, but also nutritional value of produce, sustainability of production, and ecological impact of agriculture. In accordance with its goals, NSA would benefit from applying microbial-based products as they are deemed more sustainable than their synthetic counterparts. This study characterized 3 plant-beneficial bacterial strains (Paenibacillus pasadenensis strain R16, Pseudomonas syringae strain 260-02, Bacillus amyloliquefaciens strain CC2) on their biocontrol activity and effect on nutritional and texture quality of romaine lettuce plants (Lactuca sativa) in greenhouse. The pathogens used in the trials are Rhizoctonia solani and Pythium ultimum. The obtained results indicate that strain R16 had a significant ability to cause a statistically significant reduction in the symptoms caused by both P. ultimum (reduction of 32%) and R. solani (reduction of 42%), while the other two strains showed a less efficient biocontrol ability. Indices of the nutritional quality (content in phenols, carotenoids and chlorophyll) were unaffected by the treatments, indicating that the product was equivalent to that obtained without using the bacteria, while the texture of the leaves benefits from the biocontrol treatments. In particular, the mechanical resistance of the leaves was significantly higher in non-treated plants affected by R. solani but was restored to the values of healthy plants when the bacterial inoculants were present as well. The ecological impact was evaluated by characterizing the bacterial microbiota in bulk soil, rhizosphere, and root in the presence or absence of the inoculants. The composition of the microbiota, analyzed with a Unifrac model to describe beta-diversity, was radically different in the rhizosphere and the root endosphere among treatments, while the bulk soil formed a single cluster regardless of treatment, indicating that the use of these treatments did not have an ecological impact outside of the plant.

Microbiome definition re-visited: old concepts and new challenges

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Bacillus Responses to Plant-Associated Fungal and Bacterial Communities

Some members of root-associated Bacillus species have been developed as biocontrol agents due to their contribution to plant protection by directly interfering with the growth of pathogens or by stimulating systemic resistance in their host. As rhizosphere-dwelling bacteria, these bacilli are surrounded and constantly interacting with other microbes via different types of communications. With this review, we provide an updated vision of the molecular and phenotypic responses of Bacillus upon sensing other rhizosphere microorganisms and/or their metabolites. We illustrate how Bacillus spp. may react by modulating the production of secondary metabolites, such as cyclic lipopeptides or polyketides. On the other hand, some developmental processes, such as biofilm formation, motility, and sporulation may also be modified upon interaction, reflecting the adaptation of Bacillus multicellular communities to microbial competitors for preserving their ecological persistence. This review also points out the limited data available and a global lack of knowledge indicating that more research is needed in order to, not only better understand the ecology of bacilli in their natural soil niche, but also to better assess and improve their promising biocontrol potential.

Culturable bacteria resident on lettuce might contribute to accumulation of human noroviruses

Human noroviruses (HuNoVs) are the primary non-bacterial pathogens causing acute gastroenteritis worldwide. Attachment and invasion of HuNoVs are thought to involve histo-blood group antigens (HBGAs). Romaine lettuce, which is usually consumed raw, is a common food-related vehicle for HuNoVs transmission. This study investigated the possibility that bacteria resident on the surface of lettuce leaves contribute to norovirus adherence to this food. To test this hypothesis, bacteria were isolated from romaine lettuce and screened to evaluate whether they produced any polysaccharides with structures resembling HBGAs. Twenty-seven bacterial isolates were screened and 18, belonging to 13 different genera, were found to produce HBGAs-like polysaccharides that were recognized by monoclonal antibodies specific to type A, B, H and Lewis a, b, x and y. One bacterial isolate, belonging to the genus Pseudomonas was further investigated because it produced polysaccharides with the widest range of HBGA types, including type B, H and Lewis a, b and x. The Pseudomonas HBGAs-like polysaccharides were found to be extracellular and their production was enhanced when the bacteria were cultured in oligotrophic medium. HuNoVs capture assays revealed that GI.1, GI.8, and GII.2, GII.3, GII.4, GII.6, GII.12, GII.17 genotypes can be bind to Pseudomonas HBGAs-like polysaccharides. The direct evidence of bacterial production HBGAs-like polysaccharides demonstrates one possible mechanism driving accumulation of HuNoVs on lettuce.

Microbiome-Guided Exploration of the Microbial Assemblage of the Exotic Beverage "Insect Tea" Native to Southwestern China

Insect tea is a unique beverage that is native to Southwestern China and traditionally produced by local farmers in an elaborate process. It consists of insect larvae excrements that are commonly obtained from meal moths (Pyralis farinalis Linnaeus 1758) reared on a specific plant-based diet. We have reconstructed the whole production process under laboratory conditions in order to obtain microbiome-level insights into this uncommon beverage and to trace back the origin of the prevalent bacteria in the final product. The bacterial community composition was specific for each production stage, with a high proportion of Streptomycetacea, Pseudonocaridaceae, Enterococcaceae, and Enterobacteriaceae in the insect tea. A large proportion of the constituents was traced back to the producing insect (13.2%) and its excrements (43.8%), while the initial plant-based substrate for tea production was found to contribute only 0.6% of the traceable bacteria in the final product. Moreover, an enrichment of Enterobactericeae was observed during the analyzed process steps and verified with complementary analyses. The cultivation experiments indicated a high occurrence of viable bacteria in the tea at 2.7 × 105 ± 1.2 × 105 cfu g-1. The isolated bacteria included Bordetella petrii and Enterococcus spp. that were recovered from a commercial product. By implementing an integrative approach, the insect tea was shown to harbor a species-rich bacterial community that can be traced back to certain plant and insect microbiome constituents from distinct production steps. Moreover, the microbial profile of the insect tea was found to be unique for a food product so far and contained several bacterial groups that are considered from the current perspective as food contaminants or yet unreported in other beverages. Due to the high number of viable bacteria, the tea harbors a so far undescribed dynamic component that might have implications for human health.

Re-addressing the biosafety issues of plant growth promoting rhizobacteria

To promote agronomic sustainability, extensive research is being carried out globally, investigating biofertilizer development. Recently, it has been realized that some microorganisms used as biofertilizers behave as opportunistic pathogens and belong to the biosafety level 2 (BSL-2) classification. This poses serious risk to the environmental and human health. Evidence presented in various scientific forums is increasingly favoring the merits of using BSL-2 microorganisms as biofertilizers. In this review, we emphasize that partial characterization based on traditional microbiological approaches and small subunit rRNA gene sequences/conserved regions are insufficient for the characterization of biofertilizer strains. It is advised herein, that research and industrial laboratories developing biofertilizers for commercialization or environmental release must characterize microorganisms of interest using a multilateral polyphasic approach of microbial systematics. This will determine their risk group and biosafety characteristics before proceeding with formulation development and environmental application. It has also been suggested that microorganisms belonging to risk-group-1 and BSL-1 category should be used for formulation development and for field scale applications. While, BSL-2 microorganisms should be restricted for research using containment practices compliant with strict regulations.

Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid

Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.

Bacterial communities associated with anthracnose symptomatic and asymptomatic leaves of guarana, an endogenous tropical crop, and their pathogen antagonistic effects

Plants are colonized by diverse microorganisms that can substantially impact their health and growth. Understanding bacterial diversity and the relationships between bacteria and phytopathogens may be key to finding effective biocontrol agents. We evaluated the bacterial community associated with anthracnose symptomatic and asymptomatic leaves of guarana, a typical tropical crop. Bacterial communities were assessed through culture-independent techniques based on extensive 16S rRNA sequencing, and cultured bacterial strains were evaluated for their ability to inhibit the growth of Colletotrichum sp. as well as for enzyme and siderophore production. The culture-independent method revealed that Proteobacteria was the most abundant phylum, but many sequences were unclassified. The emergence of anthracnose disease did not significantly affect the bacterial community, but the abundance of the genera Acinetobacter, Pseudomonas and Klebsiella were significantly higher in the symptomatic leaves. In vitro growth of Colletotrichum sp. was inhibited by 11.38% of the cultured bacterial strains, and bacteria with the highest inhibition rates were isolated from symptomatic leaves, while asymptomatic leaves hosted significantly more bacteria that produced amylase and polygalacturonase. The bacterial isolate Bacillus sp. EpD2-5 demonstrated the highest inhibition rate against Colletotrichum sp., whereas the isolates EpD2-12 and FD5-12 from the same genus also had high inhibition rates. These isolates were also able to produce several hydrolytic enzymes and siderophores, indicating that they may be good candidates for the biocontrol of anthracnose. Our work demonstrated the importance of using a polyphasic approach to study microbial communities from plant diseases, and future work should focus on elucidating the roles of culture-independent bacterial communities in guarana anthracnose disease.

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.)

A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO₂ fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.

Biological Control Agents Against Fusarium Wilt of Banana

In the last century, the banana crop and industry experienced dramatic losses due to an epidemic of Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f.sp. cubense (Foc) race 1. An even more dramatic menace is now feared due to the spread of Foc tropical race 4. Plant genetic resistance is generally considered as the most plausible strategy for controlling effectively such a devastating disease, as occurred for the first round of FWB epidemic. Nevertheless, with at least 182 articles published since 1970, biological control represents a large body of knowledge on FWB. Remarkably, many studies deal with biological control agents (BCAs) that reached the field-testing stage and even refer to high effectiveness. Some selected BCAs have been repeatedly assayed in independent trials, suggesting their promising value. Overall under field conditions, FWB has been controlled up to 79% by using Pseudomonas spp. strains, and up to 70% by several endophytes and Trichoderma spp. strains. Lower biocontrol efficacy (42-55%) has been obtained with arbuscular mycorrhizal fungi, Bacillus spp., and non-pathogenic Fusarium strains. Studies on Streptomyces spp. have been mostly limited to in vitro conditions so far, with very few pot-experiments, and none conducted in the field. The BCAs have been applied with diverse procedures (e.g., spore suspension, organic amendments, bioformulations, etc.) and at different stages of plant development (i.e., in vitro, nursery, at transplanting, post-transplanting), but there has been no evidence for a protocol better than another. Nonetheless, new bioformulation technologies (e.g., nanotechnology, formulation of microbial consortia and/or their metabolites, etc.) and tailor-made consortia of microbial strains should be encouraged. In conclusion, the literature offers many examples of promising BCAs, suggesting that biocontrol can greatly contribute to limit the damage caused by FWB. More efforts should be done to further validate the currently available outcomes, to deepen the knowledge on the most valuable BCAs, and to improve their efficacy by setting up effective formulations, application protocols, and integrated strategies.

Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae

The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.