A Phloem-Feeding Insect Transfers Bacterial Endophytic Communities between Grapevine Plants

Gut microbiota metagenomics and mediation of phenol degradation in Bactrocera minax (Diptera, Tephritidae)

BACKGROUND

Gut microbiota mediating insect-plant interactions have many manifestations, either by provisioning missing nutrients, or by overcoming plant defensive reactions. However, the mechanism by which gut microbiota empower insects to survive by overcoming a variety of plant secondary metabolites remains largely unknown. Bactrocera minax larvae develop in immature citrus fruits, which present numerous phenolic compounds that challenge the larvae. To explore the role of gut microbes in host use and adaptability, we uncovered the mechanisms of phenol degradation by gut microbes using metagenomic and metatranscriptomic analyses, and verified the degradation ability of isolated and cultured bacteria. Research on this subject can help develop potential strain for the environmental friendly pest management operations.

RESULTS

We demonstrated the ability of gut microbes in B. minax larvae to degrade phenols in unripe citrus. After antibiotic treatment, coniferyl alcohol and coumaric aldehyde significantly reduced the survival rate, body length and body weight of the larvae. The metagenomic and metatranscriptomic analyses in B. minax provided evidence for the presence of genes in bacteria and the related pathway involved in phenol degradation. Among them, Enterococcus faecalis and Serratia marcescens, isolated from the gut of B. minax larvae, played critical roles in phenol degradation. Furthermore, supplementation of E. faecalis and S. marcescens in artificial diets containing coniferyl alcohol and coumaric aldehyde increased the survival rate of larvae.

CONCLUSION

In summary, our results provided the first comprehensive analysis of gut bacterial communities by high-throughput sequencing and elucidated the role of bacteria in phenol degradation in B. minax, which shed light on the mechanism underlying specialist insect adaption to host secondary metabolites via gut bacteria. © 2024 Society of Chemical Industry.

The Potential of Endophytes in Improving Salt-Alkali Tolerance and Salinity Resistance in Plants

Ensuring food security for the global population is a ceaseless and critical issue. However, high-salinity and high-alkalinity levels can harm agricultural yields throughout large areas, even in largely agricultural countries, such as China. Various physical and chemical treatments have been employed in different locations to mitigate high salinity and alkalinity but their effects have been minimal. Numerous researchers have recently focused on developing effective and environmentally friendly biological treatments. Endophytes, which are naturally occurring and abundant in plants, retain many of the same characteristics of plants owing to their simultaneous evolution. Therefore, extraction of endophytes from salt-tolerant plants for managing plant growth in saline-alkali soils has become an important research topic. This extraction indicates that the soil environment can be fundamentally improved, and the signaling pathways of plants can be altered to increase their defense capacity, and can even be inherited to ensure lasting efficacy. This study discusses the direct and indirect means by which plant endophytes mitigate the effects of plant salinity stress that have been observed in recent years.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure

Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.

Isolation and Characterization of Bacterial Endophytes from Small Nodules of Field-Grown Peanut

It is evident that legume root nodules can accommodate rhizobial and non-rhizobial bacterial endophytes. Our recent nodule microbiome study in peanuts described that small nodules can harbor diverse bacterial endophytes. To understand their functional role, we isolated 87 indigenous endophytes from small nodules of field-grown peanut roots and characterized them at molecular, biochemical, and physiological levels. The amplified 16S rRNA genes and phylogenetic analysis of these isolates revealed a wide variety of microorganisms related to the genera Bacillus, Burkholderia, Enterobacter, Herbaspirillum, Mistsuaria, Pantoea, Pseudomonas, and Rhizobia. It was observed that 37% (100% identity) and 56% (>99% identity) of the isolates matched with the amplified sequence variants (ASVs) from our previous microbiome study. All of these isolates were tested for stress tolerance (high temperature, salinity, acidic pH) and phosphate (P) solubilization along with ammonia (NH3), indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and siderophore production. The majority (78%) of the isolates were found to be halotolerant, thermotolerant, and acidophilic, and a few of them showed a significant positive response to the production of IAA, NH3, siderophore, ACCD, and P-solubilization. To evaluate the plant growth promotion (PGP) activity, plant and nodulation assays were performed in the growth chamber conditions for the selected isolates from both the non-rhizobial and rhizobial groups. However, these isolates appeared to be non-nodulating in the tested conditions. Nonetheless, the isolates 2 (Pantoea), 17 (Burkholderia), 21 (Herbaspirillum), 33o (Pseudomonas), and 77 (Rhizobium sp.) showed significant PGP activity in terms of biomass production. Our findings indicate that these isolates have potential for future biotechnological applications through the development of biologicals for sustainable crop improvement.

Exchange of Microbiomes in Plant-Insect Herbivore Interactions

Prokaryotic and eukaryotic microbial symbiotic communities span through kingdoms. The vast microbial gene pool extends the host genome and supports adaptations to changing environmental conditions. Plants are versatile hosts for the symbionts, carrying microbes on the surface, inside tissues, and even within the cells. Insects are equally abundantly colonized by microbial symbionts on the exoskeleton, in the gut, in the hemocoel, and inside the cells. The insect gut is a prolific environment, but it is selective on the microbial species that enter with food. Plants and insects are often highly dependent on each other and frequently interact. Regardless of the accumulating evidence on the microbiomes of both organisms, it remains unclear how much they exchange and modify each other's microbiomes. In this review, we approach this question from the point of view of herbivores that feed on plants, with a special focus on the forest ecosystems. After a brief introduction to the subject, we concentrate on the plant microbiome, the overlap between plant and insect microbial communities, and how the exchange and modification of microbiomes affects the fitness of each host.

Glutamicibacter halophytocola-mediated host fitness of potato tuber moth on Solanaceae crops

BACKGROUND

The potato tuber moth (PTM), Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae), is a destructive pest of Solanaceae crops worldwide. α-solanine and α-chaconine are toxic steroidal glycoalkaloids (SGAs) in Solanaceae crops and are most abundant in potatoes (Solanum tuberosum L.), accounting for more than 95% of the total SGAs. PTM grows on potatoes with a higher concentration of SGAs. Gut bacteria play an important role in the physiology and behavior of insects. To understand the role of gut bacteria of PTM in host adaptability, we isolated and identified major SGA (α-chaconine and α-solanine)-degrading gut bacteria in the gut of PTM by a selective medium and analyzed their degradability and degradation mechanism.

RESULTS

The gut Glutamicibacter halophytocola S2 of PTM with high degradation capacity to α-solanine and α-chaconine were detected by liquid chromatography mass spectrometry (LC-MS) and identified by morphological and 16S rRNA gene sequence analysis. A gene cluster involving α-rhamnosidases, β-glucosidases, and β-galactosidases was identified by whole-genome sequencing of G. halophytocola S2. These genes had higher expression on the α-solanine medium. PTM inoculated with the isolated G. halophytocola S2 obtained higher fitness than antibiotic-treated PTM.

CONCLUSION

The G. halophytocola S2 in the gut of PTM could degrade the major toxic α-solanine and α-chaconine in potatoes. This enhances the fitness of PTM feeding on potatoes with high SGA contents. The results provide a theoretical foundation for the integrated pest management of PTM and provide an effective strain for the treatment of α-solanine and α-chaconine in potato food. © 2022 Society of Chemical Industry.

The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts

Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.

The secret life of insect-associated microbes and how they shape insect-plant interactions

Insects are associated with a plethora of different microbes of which we are only starting to understand their role in shaping insect–plant interactions. Besides directly benefitting from symbiotic microbial metabolism, insects obtain and transmit microbes within their environment, making them ideal vectors and potential beneficiaries of plant diseases and microbes that alter plant defenses. To prevent damage, plants elicit stress-specific defenses to ward off insects and their microbiota. However, both insects and microbes harbor a wealth of adaptations that allow them to circumvent effective plant defense activation. In the past decades, it has become apparent that the enormous diversity and metabolic potential of insect-associated microbes may play a far more important role in shaping insect–plant interactions than previously anticipated. The latter may have implications for the development of sustainable pest control strategies. Therefore, this review sheds light on the current knowledge on multitrophic insect–microbe–plant interactions in a rapidly expanding field of research.

Detection of 16SrIV-A phytoplasma DNA in Colpoptera sp. (Hemiptera: Nogodinidae) insects in Yucatan Peninsula, Mexico

Lethal yellowing (LY) is a disease that affects coconut and other palm species. It is associated to phytoplasmas of the group 16SrIV and the only reported insect vector for this pathogen so far is Haplaxius crudus. H. crudus is present in Mexico and has been associated to 16SrIV phytoplasmas, however, it was not detectable during a LY outbreak in the coast of Yucatan, Mexico, suggesting the existence of other vector species. To test this hypothesis a survey of insects was carried out and a total of 3074 insects were captured during a year of monthly sampling. Ten taxonomic orders were identified in this sample, Hemiptera being the most abundant (N=2094), and these were classified into nine families. The leafhopper Colpoptera sp. from to the Nogodinidae family was de most abundant representing 56% of the total number of insects sampled and 23% of these samples resulted positive for LY phytoplasma by PCR detection. The BLAST comparison, virtual RFLP and phylogenetic analyses of the sequenced amplicons relate the detected phytoplasma to the subgroup 16SrIV-A. The findings presented herein suggest that Colpoptera sp. could be considered as a new putative vector of the LY-causing phytoplasmas in Mexico and a candidate for further research.

Bacterial Communities in the Feces of Laboratory Reared Gampsocleis gratiosa (Orthoptera: Tettigoniidae) across Different Developmental Stages and Sexes

Simple Summary

Many insects host a diverse gut microbial community, ranging from pathogenic to obligate mutualistic organisms. Little is known about the bacteria associated with katydids. Gampsocleis gratiosa (Orthoptera, Tettigoniidae) is an economically important singing pet in China. In the present study, the bacterial communities of the laboratory-reared G. gratiosa feces were characterized using Illumina sequencing of the 16S rDNA V3-V4 region.

Abstract

We used Illumina sequencing of the 16S rDNA V3-V4 region to identify the bacterial community in laboratory-reared G. gratiosa feces across different developmental stages (1st–7th instar nymph day 0, and 0-, 7-, 14-, and 21-day adult) and sexes. In total, 14,480,559 high-quality reads were clustered into 2982 species-level operational taxonomic units (OTUs), with an average of 481.197 (±137.366) OTUs per sample. These OTUs were assigned into 25 phyla, 42 classes, 60 orders, 116 families, 241 genera, and some unclassified groups. Only 21 core OTUs were shared by all samples. The most representative phylum was Proteobacteria, followed by Firmicutes, Bacteroidetes, and Acidobacteria. At the genus level, Kluyvera (387 OTUs), Obesumbacterium (339 OTUs), Buttiauxella (296 OTUs), Lactobacillus (286 OTUs), and Hafnia (152 OTUs) were dominant bacteria. The early-instar nymphs harbored a similar bacterial community with other developmental stages, which contain higher species diversity. Both principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) failed to provide a clear clustering based on the developmental stages and sexes. Overall, we assume that G. gratiosa transmits bacteria vertically by eating contaminated eggshells, and both developmental stages and sexes had no significant effect on the fecal bacterial community.

Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari

Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites, and we determined a mite pathogenic virus (Betabaculovirus) that could be tested for using in biocontrol of agricultural pest mites.

A novel chicory fructanase can degrade common microbial fructan product profiles and displays positive cooperativity

Fructan metabolism in bacteria and plants relies on fructosyltransferases and fructanases. Plant fructanases (fructan exohydrolase, FEH) only hydrolyse terminal fructose residues. Levan (β-2,6 linkages) is the most abundant fructan type in bacteria. Dicot fructan accumulators, such as chicory (Cichorium intybus), accumulate inulin (β-2,1 linkages), harbouring several 1-FEH isoforms for their degradation. Here, a novel chicory fructanase with high affinity for levan was characterized, providing evidence that such enzymes widely occur in higher plants. It is adapted to common microbial fructan profiles, but has low affinity towards chicory inulin, in line with a function in trimming of microbial fructans in the extracellular environment. Docking experiments indicate the importance of an N-glycosylation site close to the active site for substrate specificity. Optimal pH and temperature for levan hydrolysis are 5.0 and 43.7 °C, respectively. Docking experiments suggested multiple substrate binding sites and levan-mediated enzyme dimerization, explaining the observed positive cooperativity. Alignments show a single amino acid shift in the position of a conserved DXX(R/K) couple, typical for sucrose binding in cell wall invertases. A possible involvement of plant fructanases in levan trimming is discussed, in line with the emerging 'fructan detour' concepts, suggesting that levan oligosaccharides act as signalling entities during plant-microbial interactions.

Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.)

Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry Vaccinium vitis-idaea L. and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.

Beneficial Insects Deliver Plant Growth-Promoting Bacterial Endophytes between Tomato Plants

Beneficial insects and mites, including generalist predators of the family Miridae, are widely used in biocontrol programs against many crop pests, such as whiteflies, aphids, lepidopterans and mites. Mirid predators frequently complement their carnivore diet by feeding plant sap with their piercing-sucking mouthparts. This implies that mirids may act as vectors of phytopathogenic and beneficial microorganisms, such as plant growth-promoting bacterial endophytes. This work aimed at understanding the role of two beneficial mirids (Macrolophus pygmaeus and Nesidiocoris tenuis) in the acquisition and transmission of two plant growth-promoting bacteria, Paraburkholderia phytofirmans strain PsJN (PsJN) and Enterobacter sp. strain 32A (32A). Both bacterial strains were detected on the epicuticle and internal body of both mirids at the end of the mirid-mediated transmission. Moreover, both mirids were able to transmit PsJN and 32A between tomato plants and these bacterial strains could be re-isolated from tomato shoots after mirid-mediated transmission. In particular, PsJN and 32A endophytically colonised tomato plants and moved from the shoots to roots after mirid-mediated transmission. In conclusion, this study provided novel evidence for the acquisition and transmission of plant growth-promoting bacterial endophytes by beneficial mirids.

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.

Emerging strategies for precision microbiome management in diverse agroecosystems

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.

Bacterial dispersal and biogeography as underappreciated influences on phytobiomes

Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.

Bacterial Communities Associated with the Pine Wilt Disease Insect Vector Monochamus alternatus (Coleoptera: Cerambycidae) during the Larvae and Pupae Stages

Monochamus alternatus is an important insect pest in pine forests of southern China and the dispersing vector of the pine wood nematode, Bursaphelenchus xylophilus, which leads to pine wilt disease (PWD). Microbiome of M. alternatus may contribute to survival of larvae in the host pine trees. In order to investigate the intestinal bacterial structure of M. alternatus during the larvae and pupae stages in host trees, and infer the function of symbiotic bacteria, we used 16S rRNA gene Illumina sequencing to obtain and compare the bacterial community composition in the foregut, midgut, and hindgut of larvae, pupal intestines, larval galleries, and pupal chambers of M. alternatus. The diversity of the bacterial community in larval intestines and pupal intestines were similar, as well as was significantly greater in larval galleries and pupal chambers. Although there were differences in bacterial compositions in different samples, similar components were also found. Proteobacteria and Firmicutes were the two most dominant phyla in all samples, and genera Enterobacter, Raoultella, Serratia, Lactococcus, and Pseudomonas were dominant in both the intestinal samples and plant tissue samples. Enterobacter was the most abundant genus in larval intestines, and Serratia was dominant in pupal intestine. The functions of these dominant and specific bacteria were also predicted through metagenomic analyses. These bacteria may help M. alternatus degrade cellulose and pinene. The specific role of symbiotic bacteria in the infection cycle of PWD also warrants further study in the future.

Endophytic microbial assemblage in grapevine

The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S–V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.

Midgut microbiota diversity of potato tuber moth associated with potato tissue consumed

Background

The potato tuber moth (PTM), Phthorimaea operculella (Zeller), is a worldwide pest that feeds on both the leaves and tubers of potato plants. PTM larvae can digest leaves, or tubers, resulting in serious damage to potato plants in the field and potato tubers in storage. To understand how midgut bacterial diversity is influenced by the consumption of these two tissue types, the symbiotic bacteria in the potato-feeding PTM midgut and the endophytic bacteria of potato tissues were analyzed.

Results

At the genus level, the bacterial community composition in the PTM midgut was influenced by the tissues consumed, owing to their different nutrient contents. Escherichia_Shigella and Enterobacter were the most dominant genera in the midgut of leaf-feeding and tuber-feeding PTMs, respectively. Interestingly, even though only present in low abundance in leaves and tubers, Escherichia_Shigella were dominantly distributed only in the midgut of leaf-feeding PTMs, indicating that specific accumulation of these genera have occurred by feeding on leaves. Moreover, Enterobacter, the most dominant genus in the midgut of tuber-feeding PTMs, was undetectable in all potato tissues, indicating it is gut-specific origin and tuber feeding-specific accumulation. Both Escherichia_Shigella and Enterobacter abundances were positively correlated with the dominant contents of potato leaves and tubers, respectively.

Conclusions

Enrichment of specific PTM midgut bacterial communities was related to different nutrient levels in different tissues consumed by the insect, which in turn influenced host utilization. We provide evidence that a portion of the intestinal microbes of PTMs may be derived from potato endophytic bacteria and improve the understanding of the relationship between potato endophytic bacteria and the gut microbiota of PTMs, which may offer support for integrated management of this worldwide pest.

In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.

Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

BACKGROUND

Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and community composition of microbiome associated with different plant compartments as well as bulk soils of cycad species remains elusive.

METHOD

An extensive investigation of species diversity and community composition of bacterial and fungal microbiome in roots, seeds, unfertilized seeds, ovules, pollens, and soils of Cycas panzhihuaensis L. Zhou & S. Y. Yang has been conducted by high-through sequencing technology. Moreover, principal component analysis (PCA), hierarchical cluster analysis (HCA), and heatmap analysis were applied to test the niche-specific effect and biogeography factor among different sample types of this cycad species.

RESULTS

Highly diverse microbiota and significant variation of community structure were found among different compartments of C. panzhihuaensis. Soils exhibited a remarkable differentiation of bacterial community composition compared to the other five plant organs as revealed by PCA, HCA, and heatmap analyses. Different compartments possessed unique core microbial taxa with Pseudomonadaceae and Nectriaceae shared among them. According to the indicator species analysis, there was almost no differentiation of dominant microbiomes with regard to the geography of the host cycad. Two main transmission models existed in the C. panzhihuaensis.

CONCLUSIONS

Each sample type represented a unique niche and hosted a niche-specific core microbial taxa. Contrary to previous surveys, biogeography hardly exerted impact on microbial community variation in this study. The majority of the cycad-associated microbes were horizontally derived from soils and/or air environments with the rest vertically inherited from maternal plants via seeds. This study offers a robust knowledge of plant-microbiome interaction across various plant compartments and soils and lends guidelines to the investigation of adaptation mechanism of cycads in arid and nutrient-poor environments as well as their evolutionary conservation.

The Role of the Endophytic Microbiome in the Grapevine Response to Environmental Triggers

Endophytism within Vitis represents a topic of critical relevance due to the multiple standpoints from which it can be approached and considered. From the biological and botanical perspectives, the interaction between microorganisms and perennial woody plants falls within the category of stable relationships from which the plants can benefit in multiple ways. The life cycle of the host ensures persistence in all seasons, repeated chances of contact, and consequent microbiota accumulation over time, leading to potentially high diversity compared with that of herbaceous short-lived plants. Furthermore, grapevines are agriculturally exploited, highly selected germplasms where a profound man-driven footprint has indirectly and unconsciously shaped the inner microbiota through centuries of cultivation and breeding. Moreover, since endophyte metabolism can contribute to that of the plant host and its fruits' biochemical composition, the nature of grapevine endophytic taxa identities, ecological attitudes, potential toxicity, and clinical relevance are aspects worthy of a thorough investigation. Can endophytic taxa efficiently defend grapevines by acting against pests or confer enough fitness to the plants to endure attacks? What are the underlying mechanisms that translate into this or other advantages in the hosting plant? Can endophytes partially redirect plant metabolism, and to what extent do they act by releasing active products? Is the inner microbial colonization necessary priming for a cascade of actions? Are there defined environmental conditions that can trigger the unleashing of key microbial phenotypes? What is the environmental role in providing the ground biodiversity by which the plant can recruit microsymbionts? How much and by what practices and strategies can these symbioses be managed, applied, and directed to achieve the goal of a better sustainable viticulture? By thoroughly reviewing the available literature in the field and critically examining the data and perspectives, the above issues are discussed.

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae)

The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum"

"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce's Disease Pressure

Grapevine is a pillar of the California state economy and agricultural identity. This study provides a comprehensive culture-independent microbiome analysis from the sap of grapevine overtime and in a context of a vascular disease. The vascular system plays a key role by transporting nutrient, water and signals throughout the plant. The negative pressure in the xylem conduits, and low oxygen and nutrient content of its sap make it a unique and underexplored microbial environment. We hypothesized that grapevine hosts in its sap, microbes that have a beneficial impact on plant health by protecting against pathogen attack and supporting key biological processes. To address this hypothesis, we chose a vineyard under high Pierce's disease (PD). PD is caused by the xylem-dwelling pathogenic bacterium Xylella fastidiosa. We selected ten grapevines within this vineyard with a range of disease phenotypes, and monitored them over 2 growing seasons. We sampled each vines at key phenological stages (bloom, veraison, and post-harvest) and used an amplicon metagenomics approach to profile the bacterial (16S -V4) and fungal (ITS) communities of the sap. We identified a core microbiome of the sap composed of seven bacterial (Streptococcus, Micrococcus, Pseudomonas, Bacteroides, Massilia, Acinetobacter and Bacillus) and five fungal (Cladosporium, Mycosphaerella, Alternaria, Aureobasidium, and Filobasidium) taxa that were present throughout the growing season. Overall, the sap microbial makeup collected from canes was more similar to the root microbial profile. Alpha diversity metrics indicated a microbial enrichment at bloom and in vines with moderate PD severity suggesting a host-driven microbial response to environmental cues. Beta diversity metrics demonstrated that disease condition and plant phenology impacted microbial community profiles. Our study identified several potential taxonomic targets with antimicrobial and plant growth promoting capabilities that inhabit the grapevine sap and that should be further tested as potential biological control or biofertilizer agents.

Bacteria from nodules of wild legume species: Phylogenetic diversity, plant growth promotion abilities and osmotolerance

The demand for food with high nutritional value that can sustain the growth of human population while safeguarding sustainability deserves urgent attention. A possible strategy is the inoculation of crops with plant growth promoting (PGP) bacteria. Plants are naturally colonized by bacteria that can exert beneficial effects on growth and stress tolerance. N₂ fixation by rhizobia in the root nodules of legumes is a well-known PGP effect. These bacteria can be used as inoculants to boost legumes productivity and can be especially interesting if they are able to survive to abiotic stresses, such as drought. Herein we report the phylogenetic diversity of bacteria colonizing the root nodules of several wild legume species, from four geographic locations in Portugal with different bioclimates. Interestingly, the vast majority of strains belonged to Flavobacterium, Pseudomonas and other genera apart from rhizobia. PGP abilities other than N₂ fixation (production of indol acetic acid, siderophores and volatile organic compounds) and osmotolerance were screened. Location and host plant species did not influence PGP abilities and osmotolerance. Taken together, results evidenced that bacterial strains from wild legumes displaying PGP abilities and osmotolerance can be regarded as good candidates for inoculants of a broad range of hosts, including non-legumes.

Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites

Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses Setaria viridis and Setaria pumila to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by Gammaproteobacteria, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of Gammaproteobacteria were higher in panicles, whereas Rhizobiales dominated root communities. We further identified core and non-core taxa within samples of both Setaria species. Non-core taxa included members of the Saccharibacteria and Legionelalles, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within Setaria species.

Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory

We studied the relationship between plant functional foliar traits and the endophytic bacterial communities associated in trees, taking the example of sessile oak (Quercus petraea (Matt.) Liebl). Forty-five samples with replicates of eight leaves per sample were collected in spring, summer and autumn. Bacterial community diversity was analyzed via Automated Ribosomal Intergenic Spacer Analysis (ARISA). The leaf traits specific leaf area, level of herbivory, stomatal number, stomatal length, carbon and nitrogen concentration were measured for the leaves of each sample. For statistical analysis, linear mixed effect models, the Canonical Correlation Analysis (CCA) and Non-Parametric Multivariate Analysis of Variance (NPMANOVA) were applied. Herbivory, nitrogen and carbon concentration were significantly different in autumn compared to spring and summer (p value < 0.05), while stomatal length was differentiated between spring and the other two seasons (p value < 0.01). The seasonal differentiation of the bacterial community structure was explained by the first and second axes (29.7% and 25.3%, respectively) in the CCA. The bacterial community structure significantly correlated with herbivory, nitrogen concentration and stomatal length. We conclude that herbivory, nitrogen content, and size of stomatal aperture at the leaf level are important for endophyte colonization in oaks growth in alpine forest environments.

Endosymbionts of Plant-Parasitic Nematodes

Some of the most agriculturally important plant-parasitic nematodes (PPNs) harbor endosymbionts. Extensive work in other systems has shown that endosymbionts can have major effects on host virulence and biology. This review highlights the discovery, development, and diversity of PPN endosymbionts, incorporating inferences from genomic data. Cardinium, reported from five PPN hosts to date, is characterized by its presence in the esophageal glands and other tissues, with a discontinuous distribution across populations, and genomic data suggestive of horizontal gene exchange. Xiphinematobacter occurs in at least 27 species of dagger nematode in the ovaries and gut epithelial cells, where genomic data suggest it may serve in nutritional supplementation. Wolbachia, reported in just three PPNs, appears to have an ancient history in the Pratylenchidae and displays broad tissue distribution and genomic features intermediate between parasitic and reproductive groups. Finally, a model is described that integrates these insights to explain patterns of endosymbiont replacement.

Introduction of a putative biocontrol agent into a range of phytoplasma- and liberibacter-susceptible crop plants

BACKGROUND

Phytoplasma, the causative agent of Bois Noir disease of grapevines, are vectored by the planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae). A Dyella-like bacterium (DLB) isolated from H. obsoletus inhibits the growth of Spiroplasma melliferum, a cultivable relative of phytoplasma. Additional evidence suggests that DLB can reduce the symptoms of yellows disease in grapevine plantlets. The aim of this study was to test whether DLB could colonize a range of phytoplasma- and liberibacter-sensitive crop plants, and thus assess its potential agricultural use.

RESULTS

Vitex agnus-castus, the preferred host plant of H. obsoletus was found to be a natural host of DLB, which was successfully introduced into a range of crop plants belonging to seven families. The most effective DLB application method was foliar spraying. Microscopy observation revealed that DLB aggregated on the leaf surface and around the stomata, suggesting that this is its route of entry. DLB was also present in the vascular tissues of plants, indicating that it moved systemically through the plant.

CONCLUSIONS

DLB is a potential biocontrol agent and its broad spectrum of host plants indicates the possibility of its future use against a range of diseases caused by phloem-limited bacteria. © 2017 Society of Chemical Industry.

Bacteriome from Pinus arizonica and P. durangensis: Diversity, Comparison of Assemblages, and Overlapping Degree with the Gut Bacterial Community of a Bark Beetle That Kills Pines

Symbioses between plants and microorganims have been fundamental in the evolution of both groups. The endophytic bacteria associated with conifers have been poorly studied in terms of diversity, ecology, and function. Coniferous trees of the genera Larix, Pseudotsugae, Picea and mainly Pinus, are hosts of many insects, including bark beetles and especially the Dendroctonus species. These insects colonize and kill these trees during their life cycle. Several bacteria detected in the gut and cuticle of these insects have been identified as endophytes in conifers. In this study, we characterized and compared the endophytic bacterial diversity in roots, phloem and bark of non-attacked saplings of Pinus arizonica and P. durangensis using 16S rRNA gene pyrosequencing. In addition, we evaluated the degree of taxonomic relatedness, and the association of metabolic function profiles of communities of endophytic bacteria and previously reported gut bacterial communities of D. rhizophagus; a specialized bark beetle that colonizes and kills saplings of these pine species. Our results showed that both pine species share a similar endophytic community. A total of seven bacterial phyla, 14 classes, 26 orders, 43 families, and 51 genera were identified. Enterobacteriaceae was the most abundant family across all samples, followed by Acetobacteraceae and Acidobacteriaceae, which agree with previous studies performed in other pines and conifers. Endophytic communities and that of the insect gut were significantly different, however, the taxonomic relatedness of certain bacterial genera of pines and insect assemblages suggested that some bacteria from pine tissues might be the same as those in the insect gut. Lastly, the metabolic profile using PICRUSt showed there to be a positive association between communities of both pines and insect gut. This study represents the baseline into the knowledge of the endophytic bacterial communities of two of the major hosts affected by D. rhizophagus.

Transmission of Bacterial Endophytes

Plants are hosts to complex communities of endophytic bacteria that colonize the interior of both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from the environment with each new generation, or vertically transmitted from generation to generation via seed. A better understanding of bacterial endophyte transmission routes and modes will benefit studies of plant–endophyte interactions in both agricultural and natural ecosystems. In this review, we provide an overview of the transmission routes that bacteria can take to colonize plants, including vertically via seeds and pollen, and horizontally via soil, atmosphere, and insects. We discuss both well-documented and understudied transmission routes, and identify gaps in our knowledge on how bacteria reach the inside of plants. Where little knowledge is available on endophytes, we draw from studies on bacterial plant pathogens to discuss potential transmission routes. Colonization of roots from soil is the best studied transmission route, and probably the most important, although more studies of transmission to aerial parts and stomatal colonization are needed, as are studies that conclusively confirm vertical transfer. While vertical transfer of bacterial endophytes likely occurs, obligate and strictly vertically transferred symbioses with bacteria are probably unusual in plants. Instead, plants appear to benefit from the ability to respond to a changing environment by acquiring its endophytic microbiome anew with each generation, and over the lifetime of individuals.