Plant Beneficial Microbes Research Articles

Biological control of fusarium root rot of Indian mulberry (Morinda officinalis How.) with consortia of agriculturally important microorganisms in Viet Nam

BackgroundFusarium root rot disease in Indian mulberry (Morinda officinalis How.) (FRRBK), caused by Fusarium proliferatum (FP), is widespread and responsible for serious economic losses in Viet Nam. The efficacy of a new bio-product named MICROTECH-1(NL) is compared with other commercial products for suppression of FP under in vitro, pot, nursery as well as in the field conditions.ResultsIn in vitro antagonistic assay, MICROTECH-1(NL) significantly inhibited the mycelial growth of FP (72.38%). Under pot conditions, the efficacy of all the bio-products was significantly higher when applied prior to pathogen inoculation. The disease severity of treatments with double application of MICROTECH-1(NL) (applied both in the nursery and in the pot soil) was only 15.56%, significantly lower than control (80%). Thus, the application of MICROTECH-1(NL) significantly reduced the incidence of FP and markedly increased the number of plant beneficial bacteria and actinobacteria in rhizoplane of M. officinalis compared to untreated control. In the field conditions, double application of MICROTECH-1(NL) (both in the nursery and in the field soils) significantly decreased disease severity in comparison to single application in nursery or field.ConclusionThe most effective treatment was double application of MICROTECH-1(NL), which significantly reduced the disease severity and FP population in roots of M. officinalis and increased the population of plant beneficial microbes.

Seed Coating: A Tool for Delivering Beneficial Microbes to Agricultural Crops.

Plant beneficial microbes (PBMs), such as plant growth-promoting bacteria, rhizobia, arbuscular mycorrhizal fungi, and Trichoderma, can reduce the use of agrochemicals and increase plant yield, nutrition, and tolerance to biotic–abiotic stresses. Yet, large-scale applications of PBM have been hampered by the high amounts of inoculum per plant or per cultivation area needed for successful colonization and consequently the economic feasibility. Seed coating, a process that consists in covering seeds with low amounts of exogenous materials, is gaining attention as an efficient delivery system for PBM. Microbial seed coating comprises the use of a binder, in some cases a filler, mixed with inocula, and can be done using simple mixing equipment (e.g., cement mixer) or more specialized/sophisticated apparatus (e.g., fluidized bed). Binders/fillers can be used to extend microbial survival. The most reported types of seed coating are seed dressing, film coating, and pelleting. Tested in more than 50 plant species with seeds of different dimensions, forms, textures, and germination types (e.g., cereals, vegetables, fruits, pulses, and other legumes), seed coating has been studied using various species of plant growth-promoting bacteria, rhizobia, Trichoderma, and to a lesser extent mycorrhizal fungi. Most of the studies regarding PBM applied via seed coating are aimed at promoting crop growth, yield, and crop protection against pathogens. Studies have shown that coating seeds with PBM can assist crops in improving seedling establishment and germination or achieving high yields and food quality, under reduced chemical fertilization. The right combination of biological control agents applied via seed coating can be a powerful tool against a wide number of diseases and pathogens. Less frequently, studies report seed coating being used for adaptation and protection of crops under abiotic stresses. Notwithstanding the promising results, there are still challenges mainly related with the scaling up from the laboratory to the field and proper formulation, including efficient microbial combinations and coating materials that can result in extended shelf-life of both seeds and coated PBM. These limitations need to be addressed and overcome in order to allow a wider use of seed coating as a cost-effective delivery method for PBM in sustainable agricultural systems.

Rhizosphere-Associated Pseudomonas Suppress Local Root Immune Responses by Gluconic Acid-Mediated Lowering of Environmental pH

The root microbiome consists of commensal, pathogenic, and plant-beneficial microbes [1]. Most members of the root microbiome possess microbe-associated molecular patterns (MAMPs) similar to those of plant pathogens [2]. Their recognition can lead to the activation of host immunity and suppression of plant growth due to growth-defensetradeoffs [3, 4]. We found that 42% of the tested root microbiota, including the plant growth-promoting rhizobacteria Pseudomonas capeferrum WCS358 [5, 6] and Pseudomonas simiae WCS417 [6, 7], are able to quench local Arabidopsis thaliana root immune responses that aretriggered by flg22 [8], an immunogenic epitope of the MAMP flagellin [9], suggesting that this is animportant function of the root microbiome. Ina screen for WCS358 mutants that lost their capacity to suppress flg22-induced CYP71A12pro:GUS MAMP-reporter gene expression, we identified the bacterial genes pqqF and cyoB in WCS358, which are required for the production of gluconic acid and its derivative 2-keto gluconic acid. Both WCS358 mutants are impaired in the production of these organic acids and consequently lowered their extracellular pH to a lesser extent thanwild-type WCS358. Acidification of the plant growth medium similarly suppressed flg22-induced CYP71A12pro:GUS and MYB51pro:GUS expression, and the flg22-mediated oxidative burst, suggesting a role for rhizobacterial gluconic acid-mediated modulation of the extracellular pH in the suppression of root immunity. Rhizosphere population densities of the mutants were significantly reduced compared to wild-type. Collectively, these findings show thatsuppression of immune responses is an important function of the root microbiome, as it facilitates colonization by beneficial root microbiota.

Identification and characterization of a cyclic lipopeptide iturin A from a marine-derived Bacillus velezensis 11-5 as a fungicidal agent to Magnaporthe oryzae in rice

Magnaporthe oryzae is an important rice pathogen globally. However, plant beneficial microbes and their secondary metabolites to control blast disease in rice are poorly understood. In the present study, a marine-derived Bacillus velezensis 11-5 has been characterized as an antagonist against an isolate of Magnaporthe oryzae, the causal agent of rice blast disease. A cyclic lipopeptide (CLP) iturin A has been identified from the fermentation broth of B. velezensis 11-5 by nuclear magnetic resonance spectroscopy and mass spectrometry. In addition, the in vitro and in planta biocontrol activities of CLP iturin A were evaluated in the further study, respectively. The results revealed that iturin A shows significant activity on the conidia germination and the relative appressoria formation rate of M. oryzae at the concentrations of 10 and 50 µM for 12 h and for 24 h, respectively. In addition, CLP iturin A shows the significant activity to control M. oryzae in rice plants when the concentration of the compound is higher than 10 µM. Taken all results together, this study shows that B. velezensis 11-5 has the possibility to be developed as a biopesticide to control rice blast disease in rice plants, and for the first time, this study shows a CLP iturin A produced by B. velezensis 11-5 is an agrochemical to control rice blast disease both in vitro and in rice. And therefore, the results provide information on the application of B. velezensis 11-5 and its CLP iturin A as potential biopesticides to control blast disease in rice for agricultural practice.

Identification, characterization and expression profiles of Fusarium udum stress-responsive WRKY transcription factors in Cajanus cajan under the influence of NaCl stress and Pseudomonas fluorescens OKC

The WRKY gene family has never been identified in pigeonpea (Cajanus cajan). Therefore, objective of the present study was to identify the WRKY gene family in pigeonpea and characterize the Fusarium udum stress-responsive WRKY genes under normal, NaCl-stressed and Pseudomonas fluorescens OKC (a plant growth-promoting bacterial strain) treated conditions. The aim was to characterize the Fusarium udum stress-responsive WRKY genes under some commonly occurring field conditions. We identified 97 genes in the WRKY family of pigeonpea, using computational prediction method. The gene family was then classified into three groups through phylogenetic analysis of the homologous genes from the representative plant species. Among the 97 identified WRKY genes 35 were further classified as pathogen stress responsive genes. Functional validation of the 35 WRKY genes was done through generating transcriptional profiles of the genes from root tissues of pigeonpea plants under the influence of P. fluorescens OKC after 24 h of stress application (biotic: Fusarium udum, abiotic: NaCl). The entire experiment was conducted in two pigeonpea cultivars Asha (resistant to F. udum) and Bahar (susceptible to F. udum) and the results were concluded on the basis of transcriptional regulation of the WRKY genes in both the pigeonpea cultivars. The results revealed that among the 35 tentatively identified biotic stress responsive CcWRKY genes, 26 were highly F. udum responsive, 17 were better NaCl responsive compared to F. udum and 11 were dual responsive to both F. udum and NaCl. Application of OKC was able to enhance transcript accumulation of the individual CcWRKY genes to both the stresses when applied individually but not in combined challenge of the two stresses. The results thus indicated that CcWRKY genes play a vital role in the defense signaling against F. udum and some of the F. udum responsive CcWRKYs (at least 11 in pigeonpea) are also responsive to abiotic stresses such as NaCl. Further, plant beneficial microbes such as P. fluorescens OKC also help pegionpea to defend itself against the two stresses (F. udum and NaCl) through enhanced expression of the stress responsive CcWRKY genes when the stresses are applied individually.

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages.

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

Big Data Analysis for Sustainable Agriculture on a Geospatial Cloud Framework

The grand challenge confronting agriculture is the development of technologies for sustainable intensification of crop production systems to feed the estimated future human population of 9 to 10 billion. It is thought that crop production must be increased by 60 to 100% by the year 2050 to meet these nutritional needs. Crop production systems that yield more food of higher nutritional content are needed that at the same time have a diminished impact on the environment. Prior agricultural intensification was through substantial use of fertilizer, pesticides, and irrigation all at significant environmental cost. As a part of Sustainable Agriculture, next-generation, on cropping systems that couple biologically based technologies (plant-beneficial microbes, cover crops) and precision agriculture need to be developed to decrease fertilizer, pesticide, and water inputs. Over the past two decades, Information Technology has been the disruptive force in industries by driving out market inefficiencies through automation and better decision support tools that require the inclusion of both the citizens and consumers in the process. Like all industries, Agriculture has not been immune to the constant disruptions over the past century. However, recent advances in the computing infrastructure, sensor technology, big data and advanced algorithms ( suggest that a major disruption or paradigm shift is on the horizon, leading to opportunities for sustainable agriculture entering the mainstream. Specifically, solutions based on these new technologies will be needed for mass transfer of genomic and other genetic data for development of these advanced crop cultivars, and for the management of agronomic data for the development of these next-generation production systems. Geospatial solutions based on imagery, IoT, AI, mobile data collection, etc. will be critical for the operation of precision agriculture systems where intelligent application of resource inputs are applied at precise geo-specific field locations based on crop need. Finally, solutions will be needed to allow immediate feedback from digital farm communities regarding the performance of these new cropping systems; speeding their development. Here we describe a “system of systems” approach to building a scientific network that integrates the scientific and farming communities, based on a Geoinformatics cloud framework.

Type III Secretion System of Beneficial Rhizobacteria Pseudomonas simiae WCS417 and Pseudomonas defensor WCS374.

Plants roots host myriads of microbes, some of which enhance the defense potential of plants by activating a broad-spectrum immune response in leaves, known as induced systemic resistance (ISR). Nevertheless, establishment of this mutualistic interaction requires active suppression of local root immune responses to allow successful colonization. To facilitate host colonization, phytopathogenic bacteria secrete immune-suppressive effectors into host cells via the type III secretion system (T3SS). Previously, we searched the genomes of the ISR-inducing rhizobacteria Pseudomonas simiae WCS417 and Pseudomonas defensor WCS374 for the presence of a T3SS and identified the components for a T3SS in the genomes of WCS417 and WCS374. By performing a phylogenetic and gene cluster alignment analysis we show that the T3SS of WCS417 and WCS374 are grouped in a clade that is enriched for beneficial rhizobacteria. We also found sequences of putative novel effectors in their genomes, which may facilitate future research on the role of T3SS effectors in plant-beneficial microbe interactions in the rhizosphere.

Microbes mediated plant stress tolerance in saline agricultural ecosystem

The accumulation of salts leads to assimilation of dissolved salts in the soil which results in soil salinity. Salinity affects the crop yield by reducing the levels of minerals availability, inducing ions mediated toxicity, osmotic stress, growth regulators level and reactive oxygen species production which ultimately lead to the inhibition of seed germination, seedling growth, onset of flowering, and fruit set. The beneficial microorganisms are attractive candidate to increase the agricultural productivity in saline ecosystem. The plant beneficial microbiome offers significant prospective to magnify the plant resilience and crop yields in saline agriculture systems either by modulating the uptake of ions, regulation of plant growth regulators and by the production of exopolysaccharides and alleviate the salinity stress. Salt tolerance is a complex manifestation of different physiological and biochemical events. The microbes mediated mechanisms underlying regulation of salinity responses involved in ion transport and homeostasis, osmolytes regulation, hormonal balance, antioxidant machinery and other stress signaling are critical in developing plant adaptation strategies to salinity stress. Therefore, plant beneficial microbes are attractive choice in alleviating plant stresses saline soil.

Plant-Beneficial &lt;i&gt;Pseudomonas&lt;/i&gt; Spp. Suppress Local Root Immune Responses by Gluconic Acid-Mediated Lowering of Environmental pH

The plant root microbiome consists of commensal, pathogenic and plant-beneficial microbes. Most members of the root microbiome possess microbe-associated molecular patterns (MAMPs) similar to those of plant pathogens. Their recognition by the cell surface-localized pattern recognition receptors can lead to the initiation of host immune signaling and suppression of plant growth due to growth-defense tradeoffs. We found that 42% of the tested root microbiota, including the plant growth-promoting rhizobacteria Pseudomonas capeferrum WCS358 (WCS358) and Pseudomonas simiae WCS417, are able to quench local Arabidopsis thaliana root immune responses that were triggered by the synthetic MAMP flg22, suggesting that this is an important function of the root microbiome. In a screen for WCS358 mutants that lost their capacity to suppress flg22-induced CYP71A12pro:GUS MAMP-reporter gene expression, we identified the bacterial genes pqqF and cyoB in WCS358. CyoB and pqqF are required for the production of gluconic acid and its derivative 2-keto gluconic acid. Both WCS358 mutants are impaired in the production of these organic acids and consequently lowered their extracellular pH to a lesser extent than wild-type WCS358. Acidification of the plant growth medium similarly suppressed flg22-induced CYP71A12pro:GUS and MYB51pro:GUS expression as well as the flg22-mediated oxidative burst, suggesting a role for rhizobacterial gluconic acid-mediated modulation of the extracellular pH in the suppression of local root immunity. Rhizosphere population densities of the mutants were significantly reduced compared to wild-type. Collectively, these findings show that suppression of local root immune responses is an important function of the root microbiome, as it facilitates colonization by beneficial root microbiota.

Microbial amendments alter protist communities within the soil microbiome

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

Mixed PGPR consortium: an effective modulator of antioxidant network for management of collar rot in cauliflower

Sclerotinia sclerotiorum is a cosmopolitan fungal pathogen causing stem and collar watery soft rot of cauliflower. Previous management of this disease with chemical pesticides caused hazardous results which lead to use of more eco-friendly microbial approaches. In the present study, consortia of Trichoderma harzianum TNHU27 and Pseudomonas aeruginosa PJHU15 were assessed for their ability in controlling Sclerotinia rot in cauliflower. The seedlings of cauliflower were challenged singly and in consortium with these two compatible microbes. The plants were evaluated upon challenge inoculation with S. sclerotiorum for changes in total phenolic content, the activity of defense and antioxidative enzymes. The microbial consortium comprising of T. harzianum and P. aeruginosa significantly enhanced the defense responses of the plant in comparison to pathogen challenged and unchallenged control. The study elucidates that plant beneficial microbes in the consortium may provide superior protection by induction of faster and enhanced defense responses in comparison to unchallenged and single microbe challenged plants under pathogen challenged conditions.

A simple, quick and contamination-free method for mass-multiplication of plant-beneficial microbes by small and marginal farmers using coconut water and rice gruel medium

A simple method for mass-multiplication of microbial inoculants is reported which can empower small and marginal farmers, or group of farmers, to mass-multiply by themselves plant-beneficial microbial inoculants of bacterial plant growth promoting rhizobacteria (PGPR) such as Pseudomonas spp., Bacillus spp., free-living nitrogen-fixers like Beijerinckia spp., Azotobacter spp. and phosphate solubilizing bacteria like Bacillus megaterium) and fungal antagonists/entomopathogens such as Trichoderma spp., Metarhizium anisopliae) origin. The mass-multiplication medium is based on mixture of rice gruel and mature coconut water in a set ratio, along with microgram quantities of biochar filled in pressure cooker. The method yields contamination-free liquid bioinoculant containing sufficient viable cells (as per BIS norms) within 48 hr for bacteria and 4-7 days for fungal bioinoculant for immediate application (seed or seedling treatment and soil application) by the farmers. The method requires supply of proven contaminant-free and pure bioinoculant culture to farmers in pre-filled and stoppered syringes with long needle (5 or 10 ml volume) or pre-filled ink-filler from reliable and responsible agencies for mass-multiplication. The procedure requires little technical expertise and could to a large extent emancipate farmers from depending on bioinoculants available in agriculture stores in markets, which often suffer from contamination and below par viable inoculant population.

Rhizosphere Microenvironments of Eight Common Deciduous Fruit Trees Were Shaped by Microbes in Northern China.

The rhizosphere microenvironment is the site of nutrient circulation and microbial community formation, and thus is an ongoing topic of research. Although research on this topic is extensive, studies into the rhizosphere microenvironment of fruit trees remain rare. To elucidate the mechanisms driving the fruit tree rhizosphere microenvironment, we assessed soil physicochemical properties, enzyme activities, the community-level physiological profile (CLPP) and microbial diversity in rhizospheric soils of eight common deciduous fruit trees in northern China. We found that the available minerals, pH, enzyme activities, microbial utilization of six types of carbon (C) substrates, and microbial diversity in the rhizosphere varied among tree species. Redundancy analysis (RDA) showed that rhizosphere microenvironmental parameters (ammonia nitrogen content, soil pH and invertase activity) were closely related to the soil microbial community. Further analysis revealed that the soil microbial utilization of six C sources, nitrate nitrogen content, and invertase activity were negatively correlated with Ambiguous species and Alternaria; however, these groups were positively correlated with pH. The ammonia nitrogen content was positively correlated with C source utilization and negatively correlated with Ambiguous, Lysobacter, Nitrospira, Alternaria, Fusarium, and Colletotrichum. Interestingly, invertase was closely linked to the microbial community, especially fungal diversity, and was positively correlated with plant-beneficial microbes such as Mortierella, Geomyces, Lysobacter, and Chaetomium, but negatively correlated with pathogenic microbes such as Alternaria, Fusarium, and Colletotrichum. Hence, rhizosphere soil physicochemical properties, enzyme activities and microbial community were significantly affected by tree species. Additionally, a variety of environmental factors were closely related to the microbial community in the rhizospheric soils of eight species of deciduous fruit trees.

The structure and function of the global citrus rhizosphere microbiome

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Assessment of fungal and bacterial co-inoculation on plant growth, yield and phytosterol content of Indian mustard cultivated under rainfed conditions

Inadequate monsoon influences crop productivity in sub-mountainous areas such as Kandi zone, which is characterized as a rainfed area. The present study was conducted over the period of three years (2014–17, rabi season) in rainfed area of the Kandi zone in Punjab, India. Primary focus was on the enhancement of rabi crop productivity (mustard) through application of biologically active formulation of plant beneficial microbes, Piriformospora indica alone (Pi, T1) and Pi in combination with Azotobacter chroccocum WR 5 (Pi+Az, T2). Significant improvement in plant growth and gross yield production of mustard was observed in both the treatments with maximum yield in T2 (31.3%), followed by T1 (14.6%) as compared to control. Agro-morphological traits like root length, shoot length, number of siliqua and total biomass exhibited a similar trend with T2 having maximum result followed by T1 and control. Industrially important compounds such as Beta sitosterol was present in large amount with varying concentrations in T2 (58.6%), T1 (54.5%) and control (52.3%). This study also encouraged local farmers to gain interest in sustainable agriculture through organic farming especially for mustard cultivation and demand for our commercial bio-formulation in the area has increased in the past years.

Integrated use of plant residues, phosphorus and beneficial microbes improve hybrid maize productivity in semiarid climates

Phosphorus unavailability and lack of organic matter in calcareous soils under semiarid climates are the major reasons for low crop productivity. A field experiment was conducted at The Agronomy Research Farm of The University of Agriculture Peshawar (semiarid climate), during summer 2015. The objective of the research was to investigate the effect of plant residues, organic and inorganic phosphorus management on improving yield and yield components of hybrid maize (CS-200) with (+) and without (−) phosphate solubilizing bacteria. The experiment was laid out in randomized complete block design with split plot arrangement, using three replications. A combination of plant residues and phosphorus sources were used as mainplot factor, and phosphate solubilizing bacteria were used as a subplot factor. The results revealed that plant residues, phosphorus sources and phosphate solubilizing bacteria significantly affected all parameters under study except number of plants at harvest. Application of legume residues (Faba bean) increased ear length (22.9 cm), grains row−1 (46) and ear−1 (419), 1000 grains weight (365 g), grain yield (6175 kg ha−1) and shelling percentage (83) as compared to paper mulberry and garlic residues. Phosphorus application at the higher rate of 120 kg ha−1 from inorganic source (single super phosphate) was superior in terms of higher ear length (24.4 cm), number of grains row−1 (48) and ear−1 (455), 1000 grains weight (380 g), grain yield (6558 kg ha−1), harvest index (42.7%) and shelling percentage (83%) than the lower rate of phosphorus (60 kg P ha−1). Inoculation of maize seeds with beneficial microbes (phosphate solubilizing bacteria) significantly increased ear length (22.9 cm), number of grains row−1 (45) and ear−1 (413), 1000 grains weight (364 g), grain yield (6237 kg ha−1), harvest index (41.8%) and shelling percentage (82) than without seed inoculation. On the basis of our results from this study, we concluded that application of faba bean residues, 120 kg P ha−1 as single super phosphate along with seed inoculation with phosphate solubilizing bacteria could improve yield and yield components of hybrid maize under semiarid climates.

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome.

The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.

Sustainable Agriculture—Enhancing Environmental Benefits, Food Nutritional Quality and Building Crop Resilience to Abiotic and Biotic Stresses

Feeding nutrition-dense food to future world populations presents agriculture with enormous challenges as estimates indicate that crop production must as much as double. Crop production cannot be increased to meet this challenge simply by increasing land acreage or using past agricultural intensification methods. Food production doubled in the past through substantial use of synthetic fertilizer, pesticides, and irrigation, all at significant environmental cost. Future production of nutrition-dense food will require next-generation crop production systems with decreased reliance on synthetic fertilizer and pesticide. Here, we present three case studies detailing the development of cover crops and plant-beneficial microbes for sustainable, next-generation small grain, tomato, and oilseed rape production systems. Cover crops imparted weed and pathogen control and decreased soil erosion and loss of soil nitrogen, phosphorus and carbon, while plant-beneficial microbes provided disease control and phosphorus fertility. However, yield in these next-generation crop production systems at best approximated that associated with current production systems. We argue here that to substantially increase agricultural productivity, new crop germplasm needs to be developed with enhanced nutritional content and enhanced tolerance to abiotic and biotic stress. This will require using all available technologies, including intensified genetic engineering tools, in the next-generation cropping systems.

Microbial small molecules - weapons of plant subversion.

Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.