Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa.

Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3-V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1-37.43%), Bacillus (4.5-20.4%), Rhizobium (1.4-6.5%), and Devosia (1.5-6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79-41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).

Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa.

Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and ß-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.

Comparative Transcriptome and Expression Profiling of Resistant and Susceptible Banana Cultivars during Infection by Fusarium oxysporum.

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases of banana. Methods to control the disease are still inadequate. The present investigation targeted expression of defense-related genes in tissue cultured banana plantlets of Fusarium resistant and susceptible cultivars after infection with biological control agents (BCAs) and Fusarium (Foc race 1). In total 3034 differentially expressed genes were identified which annotated to 58 transcriptional families (TF). TF families such as MYB, bHLH and NAC TFs were mostly up-regulated in response to pathogen stress, whereas AP2/EREBP were mostly down-regulated. Most genes were associated with plant-pathogen response, plant hormone signal transduction, starch and sucrose metabolism, cysteine and methionine metabolism, flavonoid biosynthesis, selenocompound metabolism, phenylpropanoid biosynthesis, mRNA surveillance pathway, mannose type O-glycan biosynthesis, amino acid and nucleotide sugar metabolism, cyanoamino acid metabolism, and hormone signal transduction. Our results showed that the defense mechanisms of resistant and susceptible banana cultivars treated with BCAs, were regulated by differentially expressed genes in various categories of defense pathways. Furthermore, the association with different resistant levels might serve as a strong foundation for the control of Fusarium wilt of banana.

Insights Into Microbially Induced Salt Tolerance and Endurance Mechanisms (STEM) in Plants.

Salt stress threatens the achievement of sustainable global food security goals by inducing secondary stresses, such as osmotic, ionic, and oxidative stress, that are detrimental to plant growth and productivity. Various studies have reported the beneficial roles of microbes in ameliorating salt stress in plants. This review emphasizes salt tolerance and endurance mechanisms (STEM) in microbially inoculated (MI) plants that ensure plant growth and survival. Well-established STEM have been documented in MI plants and include conglomeration of osmolytes, antioxidant barricading, recuperating nutritional status, and ionic homeostasis. This is achieved via involvement of P solubilization, siderophore production, nitrogen fixation, selective ion absorption, volatile organic compound production, exopolysaccharide production, modifications to plant physiological processes (photosynthesis, transpiration, and stomatal conductance), and molecular alterations to alter various biochemical and physiological processes. Salt tolerance and endurance mechanism in MI plants ensures plant growth by improving nutrient uptake and maintaining ionic homeostasis, promoting superior water use efficiency and osmoprotection, enhancing photosynthetic efficiency, preserving cell ultrastructure, and reinforcing antioxidant metabolism. Molecular research in MI plants under salt stress conditions has found variations in the expression profiles of genes such as HKT1, NHX, and SOS1 (ion transporters), PIPs and TIPs (aquaporins), RBCS, RBCL (RuBisCo subunits), Lipoxygenase2 [jasmonic acid (JA) signaling], ABA (abscisic acid)-responsive gene, and APX, CAT, and POD (involved in antioxidant defense). Proteomic analysis in arbuscular mycorrhizal fungi-inoculated plants revealed upregulated expression of signal transduction proteins, including Ca2+ transporter ATPase, calcium-dependent protein kinase, calmodulin, and energy-related proteins (NADH dehydrogenase, iron-sulfur protein NADH dehydrogenase, cytochrome C oxidase, and ATP synthase). Future research should focus on the role of stress hormones, such as JA, salicylic acid, and brassinosteroids, in salt-stressed MI plants and how MI affects the cell wall, secondary metabolism, and signal transduction in host plants.

Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions.

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa.

Metagenomic Insights of the Root Colonizing Microbiome Associated with Symptomatic and Non-Symptomatic Bananas in Fusarium Wilt Infected Fields.

Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and their potential role in disease development has not been explored so far. Roots from symptomatic and non-symptomatic banana plants were sampled from fields infected by Fusarium oxysporum f.sp. cubense race 1. The goal was to compare the endophytic microbiota between symptomatic and non-symptomatic plants through high throughput sequencing of 16s rDNA and shotgun metagenome sequencing. The results revealed that the endophytic root microbiome in bananas is dominated by Proteobacteria and Bacteroidetes followed to a lesser extent by Actinobacteria. The development of disease greatly impacted the endophytic microbial communities. For example, Flavobacteriales abundance was correlated with symptom development.

Corrigendum: Biological Control Agents Against Fusarium Wilt of Banana.

[This corrects the article DOI: 10.3389/fmicb.2019.00616.].

Microbes in Cahoots with Plants: MIST to Hit the Jackpot of Agricultural Productivity during Drought.

Drought conditions marked by water deficit impede plant growth thus causing recurrent decline in agricultural productivity. Presently, research efforts are focussed towards harnessing the potential of microbes to enhance crop production during drought. Microbial communities, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) buddy up with plants to boost crop productivity during drought via microbial induced systemic tolerance (MIST). The present review summarizes MIST mechanisms during drought comprised of modulation in phytohormonal profiles, sturdy antioxidant defence, osmotic grapnel, bacterial exopolysaccharides (EPS) or AMF glomalin production, volatile organic compounds (VOCs), expression of fungal aquaporins and stress responsive genes, which alters various physiological processes such as hydraulic conductance, transpiration rate, stomatal conductivity and photosynthesis in host plants. Molecular studies have revealed microbial induced differential expression of various genes such as ERD15 (Early Response to Dehydration 15), RAB18 (ABA-responsive gene) in Arabidopsis, COX1 (regulates energy and carbohydrate metabolism), PKDP (protein kinase), AP2-EREBP (stress responsive pathway), Hsp20, bZIP1 and COC1 (chaperones in ABA signalling) in Pseudomonas fluorescens treated rice, LbKT1, LbSKOR (encoding potassium channels) in Lycium, PtYUC3 and PtYUC8 (IAA biosynthesis) in AMF inoculated Poncirus, ADC, AIH, CPA, SPDS, SPMS and SAMDC (polyamine biosynthesis) in PGPR inoculated Arabidopsis, 14-3-3 genes (TFT1-TFT12 genes in ABA signalling pathways) in AMF treated Solanum, ACO, ACS (ethylene biosynthesis), jasmonate MYC2 gene in chick pea, PR1 (SA regulated gene), pdf1.2 (JA marker genes) and VSP1 (ethylene-response gene) in Pseudomonas treated Arabidopsis plants. Moreover, the key role of miRNAs in MIST has also been recorded in Pseudomonas putida RA treated chick pea plants.

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.

Field Based Assessment of Capsicum annuum Performance with Inoculation of Rhizobacterial Consortia.

Plant growth promoting rhizobacteria (PGPR) are associated with plant roots and augment plant productivity and immunity by reducing fertilizer application rates and nutrient runoff. Studies were conducted to evaluate bell pepper transplants amended with formulation of consortium of two indigenous PGPR isolates (Bacillus subtilis and Bacillus pumilus) in terms of increase in yield and disease resistance under field conditions. Transplants were planted into plots treated by NPK (nitrogen, phosphorus and potassium), fungicides, soil solarization, MeBr fumigation, PGPR and untreated soil. Treatments were assessed for incidence of soil-borne phytopathogens viz. Phytophthora capsici and Colletotrichum sp. Highly significant increases in bell pepper transplant growth occurred in response to formulations of PGPR isolates. Transplant vigor and survival in the field were also improved by PGPR treatments. Consortium of Bacillus subtilis and Bacillus pumilus reduced disease incidence of damping off by 1.81% and anthracnose by 1.75%. Numbers of colony forming units of Phytophthora capsici and Colletotrichum sp. were significantly higher in all plots than those treated with PGPR consortium. Incidence of seed rot and seedling blight on bell pepper was significantly lower in PGPR-treated plots and highest in untreated plots. Total fruit yield of bell pepper increased by 379.36% with PGPR consortium (Bacillus subtilis and Bacillus pumilus).

Bacillus pumilus strain YSPMK11 as plant growth promoter and bicontrol agent against Sclerotinia sclerotiorum.

A study was executed in a direction to attenuate Sclerotinia stalk rot (SSR) disease through biocontrol agent and also to enhance crop productivity. Culture filtrate of bacterial strain YSPMK11 inhibited growth of Sclerotinia sclerotiorum in vitro which also exhibited higher plant growth promoting attributes. Interaction studies revealed maximum (81.50%) growth inhibition at 35 °C and pH 7.0 after 72 h incubation period with 15% culture filtrate. Based upon 16S rRNA gene sequence strain, YSPMK11 was identified as Bacillus pumilus. Furthermore, the genome of this isolate was searched for antimicrobial lipopeptide, i.e., ItuD and SrfC genes. The PCR amplification results showed the presence of both these lipopeptide genes in isolate YSPMK11. Iturin A as antifungal compound was identified as major components of fraction through GC/MS. In field experiments, the application of strain YSPMK11 cell suspension (108 CFU/ml) suppressed disease severity by 93% and increased curd yield by 36% which was more that of commercially used fungicide in farmer practices under mid-hills of Himachal Pradesh. Conclusively, our study is first to demonstrate the effect of B. pumilus strain YSPMK11 in suppression of SSR under field conditions and would be employed as an efficient biocontrol agent to replace commercial fungicides in cauliflower cropping system. In addition, the presence of both lipopeptide genes (ItuD and SrfC) and iturin A in this isolate makes him potent strain for biological control application in agriculture.