Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil

Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant

Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes.

IMPORTANCE

There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.

Water Stress and Black Cutworm Feeding Modulate Plant Response in Maize Colonized by Metarhizium robertsii

Plants face many environmental challenges and have evolved different strategies to defend against stress. One strategy is the establishment of mutualistic associations with endophytic microorganisms which contribute to plant defense and promote plant growth. The fungal entomopathogen Metarhizium robertsii is also an endophyte that can provide plant-protective and growth-promoting benefits to the host plant. We conducted a greenhouse experiment in which we imposed stress from deficit and excess soil moisture and feeding by larval black cutworm (BCW), Agrotis ipsilon, to maize plants that were either inoculated or not inoculated with M. robertsii (Mr). We evaluated plant growth and defense indicators to determine the effects of the interaction between Mr, maize, BCW feeding, and water stress. There was a significant effect of water treatment, but no effect of Mr treatment, on plant chlorophyl, height, and dry biomass. There was no effect of water or Mr treatment on damage caused by BCW feeding. There was a significant effect of water treatment, but not Mr treatment, on the expression of bx7 and rip2 genes and on foliar content of abscisic acid (ABA), 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and gibberellin 19 (GA19), whereas GA53 was modulated by Mr treatment. Foliar content of GA19 and cis-Zeatin (cZ) was modulated by BCW feeding. In a redundancy analysis, plant phenology, plant nutrient content, and foliar DIMBOA and ABA content were most closely associated with water treatments. This study contributes toward understanding the sophisticated stress response signaling and endophytic mutualisms in crops.

Ralstonia solanacearum differentially modulates soil physicochemical properties and rhizospheric bacteriome of resistant and susceptible tobacco cultivars

Ralstonia solanacearum is a devastating soilborne pathogen which poses significant yield and economic losses to tobacco production globally. The impact of R. solanacearum on rhizosphere bacteriome and soil physicochemical characteristics in resistant and susceptible tobacco cultivars is poorly understood. This study aims to determine the effect of R. solanacearum on soil physicochemical parameters and rhizosphere bacteriome of resistant (K326) and susceptible (Hongda) tobacco cultivars at various growth stages. Results demonstrated that the contents of available potassium and phosphorus, as well as soil pH were significantly increased in K326 soils (CK and T2) compared with Hongda (T1) after 21, 42, and 63 days post-inoculation (dpi) of R. solanacearum except for available nitrogen which showed an opposite trend. The qPCR results showed a significant decrease in R. solanacearum population in rhizosphere of K326 (T2) compared to the Hongda (T1) at 21 and 63 dpi than that after 42 dpi. The rhizosphere bacteriome analysis through 16S rRNA amplicon sequencing revealed that rhizosphere bacterial community composition was significantly different between two tobacco cultivars (Hongda and K326) and this effect was more prominent after 63 dpi (93 days after post-transplantation), suggesting that each cultivar recruits a unique set of bacterial communities. There was no obvious difference observed in the rhizosphere bacteriome of CK (K326) and T2 (K326), which might be attributed to the same genetic makeup and inherent resistance of K326 to bacterial wilt infection. Analysis of co-occurrence networks revealed that the microbial network in T1 (Hongda) was more complex than those in T2 (K326) and CK (K326), while the networks in CK and T2 were almost identical. The present research highlights the time-course relationship between environmental factors and rhizosphere bacteriome of tobacco cultivars showing different levels of resistance against R. solanacearum. Conclusively, studying the plant-soil-microbe interaction system in susceptible and resistant tobacco cultivars may enable us to develop effective integrated disease control plans for the healthy production of tobacco crops.

Maize response to endophytic Metarhizium robertsii is altered by water stress

To defend against damage from environmental stress, plants have evolved strategies to respond to stress efficiently. One such strategy includes forming mutualist relationships with endophytes which confer stress-alleviating plant defensive and growth promoting effects. Metarhizium robertsii is an entomopathogen and plant-protective and growth-promoting endophyte. To determine the context dependency of the relationship between M. robertsii and maize, we conducted a greenhouse experiment that imposed stress as deficit and excess soil moisture on maize plants which were inoculated or not inoculated with M. robertsii and measured plant growth and defense indicators. Maize height and endophytic root colonization by M. robertsii were positively correlated in the deficit water treatment, but not in the adequate or excess water treatments. The relative expression of ZmLOX1 in the jasmonic acid (JA) biosynthesis pathway was significantly greater in M. robertsii-inoculated than in non-inoculated plants, but water treatment had no effect. There was significant interaction between M. robertsii and water treatments on foliar concentrations of JA and jasmonoyl isoleucine (JA-ILE), suggesting that water stress impacts M. robertsii as a modulator of plant defense. Water stress, but not inoculation with M. robertsii, had a significant effect on the expression of MYB (p = 0.021) and foliar concentrations of abscisic acid (p<0.001), two signaling molecules associated with abiotic stress response. This study contributes toward understanding the highly sophisticated stress response signaling network and context dependency of endophytic mutualisms in crops.

Enhanced production of select phytocannabinoids in medical Cannabis cultivars using microbial consortia

The root microbiome of medical cannabis plants has been largely unexplored due to past legal restrictions in many countries. Microbes that live on and within the tissue of Cannabis sativa L. similar to other plants, provide advantages such as stimulating plant growth, helping it absorb minerals, providing protection against pathogen attacks, and influencing the production of secondary metabolites. To gain insight into the microbial communities of C. sativa cultivars with different tetrahydrocannabinol (THC) and cannabidiol (CBD) profiles, a greenhouse trial was carried out with and without inoculants added to the growth substrate. Illumina MiSeq metabarcoding was used to analyze the root and rhizosphere microbiomes of the five cultivars. Plant biomass production showed higher levels in three of five cultivars inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis and microbial suspension. The blossom dry weight of the cultivar THE was greater when inoculated with R. irregularis and microbial suspension than with no inoculation. Increasing plant biomass and blossom dry weight are two important parameters for producing cannabis for medical applications. In mature Cannabis, 12 phytocannabinoid compounds varied among cultivars and were affected by inoculants. Significant differences (p ≤ 0.01) in concentrations of cannabidivarinic acid (CBDVA), cannabidivarin (CBDV), cannabigerol (CBG), cannabidiol (CBD), and cannabigerolic acid (CBGA) were observed in all Cannabis cultivars when amended with F, K1, and K2 inoculants. We found microbes that were shared among cultivars. For example, Terrimicrobium sp., Actinoplanes sp., and Trichoderma reesei were shared by the cultivars ECC-EUS-THE, CCL-ECC, and EUS-THE, respectively. Actinoplanes sp. is a known species that produces phosphatase enzymes, while Trichoderma reesei is a fungal train that produces cellulase and contributes to organic matter mineralization. However, the role of Terrimicrobium sp. as an anaerobic bacterium remains unknown. This study demonstrated that the use of inoculants had an impact on the production of phytocannabinoids in five Cannabis cultivars. These inoculants could have useful applications for optimizing cannabis cultivation practices and increasing the production of phytocannabinoids.

Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies

Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N₂, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth.

Integrated Pest Management of Wireworms (Coleoptera: Elateridae) and the Rhizosphere in Agroecosystems

The rhizosphere is where plant roots, physical soil, and subterranean organisms interact to contribute to soil fertility and plant growth. In agroecosystems, the nature of the ecological interactions within the rhizosphere is highly dynamic due to constant disruptions from agricultural practices. The concept of integrated pest management (IPM) was developed in order to promote an approach which is complementary to the environment and non-target organisms, including natural enemies, by reducing the sole reliance on synthetic pesticides to control pests. However, some of the implemented integrated cultural and biological control practices may impact the rhizosphere, especially when targeting subterranean pests. Wireworms, the larval stage of click beetles (Coleoptera: Elateridae), are generalist herbivores and a voracious group of pests that are difficult to control. This paper introduces some existing challenges in wireworm IPM, and discusses the potential impacts of various control methods on the rhizosphere. The awareness of the potential implications of different pest management approaches on the rhizosphere will assist in decision-making and the selection of the control tactics with the least long-term adverse effects on the rhizosphere.

Antimicrobial Volatiles of the Insect Pathogen Metarhizium brunneum

Fungal volatile organic compounds (VOCs) represent promising candidates for biopesticide fumigants to control crop pests and pathogens. Herein, VOCs produced using three strains of the entomopathogenic fungus Metarhizium brunneum were identified via GC-MS and screened for antimicrobial activity. The VOC profiles varied with fungal strain, development state (mycelium, spores) and culture conditions. Selected VOCs were screened against a range of rhizosphere and non-rhizosphere microbes, including three Gram-negative bacteria (Escherichia coli, Pantoea agglomerans, Pseudomonas aeruginosa), five Gram-positive bacteria (Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, B. megaterium, B. thuringiensis), two yeasts (Candida albicans, Candida glabrata) and three plant pathogenic fungi (Pythium ultimum, Botrytis cinerea, Fusarium graminearum). Microbes differed in their sensitivity to the test compounds, with 1-octen-3-ol and isovaleric acid showing broad-spectrum antimicrobial activity. Yeasts and bacteria were inhibited by the same VOCs. Cryo-SEM showed that both yeasts and bacteria underwent some form of “autolysis”, where all components of the cell, including the cell wall, disintegrated with little evidence of their presence in the clear, inhibition zone. The oomycete (P. ultimum) and ascomycete fungi (F. graminearum, B. cinerea) were sensitive to a wider range of VOCs than the bacteria, suggesting that eukaryotic microbes are the main competitors to M. brunneum in the rhizosphere. The ability to alter the VOC profile in response to nutritional cues may assist M. brunneum to survive among the roots of a wide range of plant species. Our VOC studies provided new insights as to how M. brunneum may protect plants from pathogenic microbes and correspondingly promote healthy growth.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish

The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.

Engineering the plant microbiota in the context of the theory of ecological communities

Crop-associated microorganisms are known to have a determining influence on crop growth and resistance to stresses. Indeed, microorganisms can deter pathogens, reduce stress levels, improve nutrition, and stimulate growth. However, the microbial communities associated with a plant are rarely optimal for agricultural needs. But how can we engineer crops-associated microbial communities? An interesting framework to address this question is the theory of ecological communities that stipulates four processes by which communities can change: 1) selection, 2) dispersal, 3) speciation and 4) ecological drift. Of these, speciation and dispersal can result in the addition of new species to the plant microbiota, whereas selection and drift can lead to the loss of species. We believe that if these mechanisms are sufficiently understood, they could be harnessed to purposefully engineer the crop microbiota. Here, we will discuss the recent efforts to modify the phenotype of plants that are aligned with these ecological processes.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Can Potato Plants Be Colonized with the Fungi Metarhizium and Beauveria under Their Natural Load in Agrosystems?

Beauveria and Metarhizium fungi are facultative plant endophytes that provide plant growth-stimulating, immunomodulatory, and other beneficial effects. However, little is known about the level of plant colonization by these fungi under natural conditions. We assessed the endophytic colonization of potatoes (Solanum tuberosum) with entomopathogenic fungi at their natural load in soils (102-104 colony-forming units per g). Microbiological analyses of soils and plant organs, as well as a metagenomic analysis of potato roots and leaves, were conducted in three locations in Western Siberia, consisting of conventional agrosystems and kitchen gardens. The fungi were isolated at a relatively high frequency from unsterilized roots (up to 53% of Metarhizium-positive plants). However, the fungi were sparsely isolated from the internal tissues of roots, stems, and leaves (3%). Among the genus Metarhizium, two species, M. robertsii and M. brunneum, were detected in plants as well as in soils, and the first species was predominant. A metagenomic analysis of internal potato tissues showed a low relative abundance of Beauveria and Metarhizium (<0.3%), and the communities were represented primarily by phytopathogens. We suggest that colonization of the internal tissues of potatoes occurs sporadically under a natural load of entomopathogenic fungi in soils. The lack of stable colonization of potato plants with Beauveria and Metarhizium may be due to competition with phytopathogens.

Geographical Isolation and Root-Associated Fungi in the Marine Terrains: A Step Toward Establishing a Strategy for Acquiring Unique Microbial Resources

This study aimed to understand whether the geo-ecological segregation of native plant species affects the root-associated fungal community. Rhizoplane (RP) and rhizosphere (RS) fungal microbiota of Sedum takesimense native to three geographically segregated coastal regions (volcanic ocean islands) were analyzed using culture-independent methods: 568,507 quality sequences, 1399 operational taxonomic units, five phyla, and 181 genera were obtained. Across all regions, significant differences in the phyla distribution and ratio were confirmed. The Chao's richness value was greater for RS than for RP, and this variance coincided with the number of genera. In contrast, the dominance of specific genera in the RS (Simpson value) was lower than the RP at all sites. The taxonomic identity of most fungal species (95%) closely interacting with the common host plant was different. Meanwhile, a considerable number of RP only residing fungal genera were thought to have close interdependency on their host halophyte. Among these, Metarhizium was the sole genus common to all sites. These suggest that the relationship between potential symbiotic fungi and their host halophyte species evolved with a regional dependency, in the same halophyte species, and of the same natural habitat (volcanic islands); further, the fungal community differenced in distinct geographical regions. Importantly, geographical segregation should be accounted for in national culture collections, based on taxonomical uniqueness.

Innovative granular formulation of Metarhizium robertsii microsclerotia and blastospores for cattle tick control

The tick Rhipicephalus microplus poses a serious threat to the cattle industry, resulting in economic losses aggravated by tick resistance to chemical acaricides. Strains of Metarhizium spp., a well-known group of entomopathogenic fungi, can contribute to managing this ectoparasite. We explored two novel granular, microsclerotia- or blastospores-based formulations of Metarhizium robertsii for R. microplus control under semi-field conditions. Fungal persistence in soil was also observed for 336 days. The experiment used pots of Urochloa decumbens cv. Basilisk grass, treated with 0.25 or 0.5 mg of granular formulation/cm2 (25 or 50 kg/ha) applied to the soil surface prior to transferring engorged tick females onto the treated soil. The fungal granules yielded more conidia with subsequent sporulation under controlled indoor conditions than in the outdoor environment, where the levels of fungus rapidly declined over time. Metarhizium-root colonization ranged from 25 to 66.7% depending on the propagule and rate. Fungal formulations significantly reduced the number of tick larvae during the humid season, reaching at least 64.8% relative efficacy. Microsclerotia or blastospores-granular formulations of M. robertsii can reduce the impact of R. microplus, and thus prove to be a promising tool in the control of ticks.

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

The multifunctional lifestyles of Metarhizium: evolution and applications

The genus Metarhizium is comprised of a diverse group of common soil fungi that exhibit multifunctional lifestyles with varying degrees of saprotrophic, endophytic, and insect pathogenic modes of nutrient acquisition. The transcriptome of these species is modulated to reflect immediate needs of the fungus and availability of resources-a form of transcriptional plasticity that allows for physiological adaptation to environments with diverse and dynamic exploitable nutrient sources. In this review, we discuss the endophytic, insect pathogenic lifestyles of Metarhizium spp., including their symbiotic interface, origins, and evolution, and agricultural applications. Isotope labeling experiments have demonstrated that a mutually beneficial exchange of limiting nutrients occurs between the fungus and its host plant, with nitrogen derived via insect pathogenesis being translocated from Metarhizium to host plants in exchange for fixed carbon in the form of photosynthate. Thus, the endophytic and entomopathogenic abilities of Metarhizium spp. are not exclusive of one another, but rather are interdependent and reciprocal in nature. Although endophytic, insect pathogenic fungi (EIPF) could certainly have evolved from insect pathogenic fungi, phylogenomic evidence indicates that this genus is more closely related to plant-associated fungi than animal pathogens, suggesting that Metarhizium evolved from a lineage of plant symbionts, which subsequently acquired genes for insect pathogenesis. Entomopathogenicity may have been an adaptive trait, allowing for procurement of insect-derived nitrogen that could be translocated to host plants and bartered for fixed carbon, thereby improving the stability of fungal-plant symbioses. Given their ability to simultaneously parasitize soil insects, including a number of pests of agriculturally important crops, as well as promote plant health, growth, and productivity, Metarhizium spp. are considered promising alternatives to the chemical pesticides and fertilizers that have wreaked havoc on the health and integrity of ecosystems. KEY POINTS: • Metarhizium is a fungus that is an insect pathogen as well as a plant symbiont. • The genus Metarhizium has specialist and generalist insect pathogens. • Metarhizium is phylogenetically most closely related to plant endophytes.

Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum

A Gram-staining-negative non endospore-forming strain, PXU-55^T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium. The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the PXU-55^T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% (Flavobacterium defluvii), and 86.1 and 29.9% (Flavobacterium johnsoniae). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C_15:0, iso-C_15:0 3-OH, iso-C_17:0 3-OH, C_15:0, summed feature 3 (C_16:1ω7c and/or iso-C_15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C_16:0 3-OH, C_16:0 3-OH and C_15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium. Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55^T (=CIP 111646^T=CCM 8914^T) represents a novel species with the name Flavobacterium panici sp. nov.

Localization of the insect pathogenic fungal plant symbionts Metarhizium robertsii and Metarhizium brunneum in bean and corn roots

Metarhizium is an insect pathogenic fungus and a plant root symbiont. Here the root association patterns (rhizoplane or endophytic colonization) were analyzed in common beans (Phaseolus vulgaris) and sweet corn (Zea mays) using M. robertsii and M. brunneum under various vermiculite treatments (control, with sucrose, with an insect) at two time points of plant growth (10 and 20 days). We observed that M. brunneum and M. robertsii preferentially endophytically colonized the hypocotyl, however, greater rhizoplane colonization was observed at the regions proximal to the hypocotyl in both plants. Vermiculite amended with an infected insect resulted in greater endophytic and rhizoplane colonization at 20 days compared to 10 days, for both plants as well as for both Metarhizium species. Regardless of the vermiculite treatment, corn was preferentially colonized compared to bean. Sucrose amendment in the vermiculite and infected insect amended vermiculite only showed differences in rhizoplane colonization. The greatest root association occurred with M. brunneum with an infected insect and that in corn after 20 days.