Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis

How host species and body part determine the microbial communities of five ambrosia beetle species

The ambrosia beetles are farming insects that feed mainly on their cultivated fungi, which in some occasions are pathogens from forest and fruit trees. We used a culture-independent approach based on 16S and 18S rRNA gene metabarcoding analysis to investigate the diversity and composition of the bacterial and fungal communities associated with five ambrosia beetle species: four species native to America (Monarthrum dimidiatum, Dryocoetoides capucinus, Euwallacea discretus, Corthylus consimilis) and an introduced species (Xylosandrus morigerus). For the bacterial community, the beetle species hosted a broad diversity with 1,579 amplicon sequence variants (ASVs) and 66 genera, while for the fungal community they hosted 288 ASVs and 39 genera. Some microbial groups dominated the community within a host species or a body part (Wolbachia in the head-thorax of E. discretus; Ambrosiella in the head-thorax and abdomen of X. morigerus). The taxonomic composition and structure of the microbial communities appeared to differ between beetle species; this was supported by beta-diversity analysis, which indicated that bacterial and fungal communities were clustered mainly by host species. This study characterizes for the first time the microbial communities associated with unexplored ambrosia beetle species, as well as the factors that affect the composition and taxonomic diversity per se, contributing to the knowledge of the ambrosia beetle system.

Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae)

The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.

Erwiniaceae bacteria play defensive and nutritional roles in two widespread ambrosia beetles

Ambrosia beetles are fungal-growing insects excavating galleries deep inside the wood. Their success as invaders increased scientific interest towards them. However, most studies on their microbiota targeted their fungal associates whereas the role of bacterial associates is understudied. To explore the role of abundant microbial associates, we isolated bacteria from active galleries of two widespread ambrosia beetles, Xylosandrus crassiusculus and X. germanus. These isolates were classified within the Erwiniaceae family and through a phylogenetic analysis including isolates from other insects we showed that they clustered with isolates obtained from ambrosia and bark beetles, including Erwinia typographi. The whole genome analysis of the isolate from active galleries of X. crassiusculus suggested that this bacterium plays both a nutritional role, by providing essential amino acids and enzymes for the hydrolysis of plant biomass, and a defensive role, by producing antibiotics. This defensive role was also tested in vitro against fungi, including mutualists, common associates, and parasites. The bacteria inhibited the growth of some of the common associates and parasites but did not affect mutualists. Our study supported the hypothesis of a mutualist role of Erwiniaceae bacteria in ambrosia beetles and highlighed the importance of bacteria in maintaining the symbiosis of their host with nutritional fungi.

The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus

Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.

Impact of transgenerational host switch on gut bacterial assemblage in generalist pest, Spodoptera littoralis (Lepidoptera: Noctuidae)

Diet composition is vital in shaping gut microbial assemblage in many insects. Minimal knowledge is available about the influence of transgenerational diet transition on gut microbial community structure and function in polyphagous pests. This study investigated transgenerational diet-induced changes in Spodoptera littoralis larval gut bacteriome using 16S ribosomal sequencing. Our data revealed that 88% of bacterial populations in the S. littoralis larval gut comprise Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The first diet transition experiment from an artificial diet (F0) to a plant diet (F1), cabbage and cotton, caused an alteration of bacterial communities in the S. littoralis larval gut. The second transgenerational diet switch, where F1 larvae feed on the same plant in the F2 generation, displayed a significant variation suggesting further restructuring of the microbial communities in the Spodoptera larval gut. F1 larvae were also challenged with the plant diet transition at the F2 generation (cabbage to cotton or cotton to cabbage). After feeding on different plant diets, the microbial assemblage of F2 larvae pointed to considerable differences from other F2 larvae that continued on the same diet. Our results showed that S. littoralis larval gut bacteriome responds rapidly and inexplicably to different diet changes. Further experiments must be conducted to determine the developmental and ecological consequences of such changes. Nevertheless, this study improves our perception of the impact of transgenerational diet switches on the resident gut bacteriome in S. littoralis larvae and could facilitate future research to understand the importance of symbiosis in lepidopteran generalists better.

Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06

Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.

Comparing the succession of microbial communities throughout development in field and laboratory nests of the ambrosia beetle Xyleborinus saxesenii

Some fungus-farming ambrosia beetles rely on multiple nutritional cultivars (Ascomycota: Ophiostomatales and/or yeasts) that seem to change in relative abundance over time. The succession of these fungi could benefit beetle hosts by optimal consumption of the substrate and extended longevity of the nest. However, abundances of fungal cultivars and other symbionts are poorly known and their culture-independent quantification over development has been studied in only a single species. Here, for the first time, we compared the diversity and succession of both fungal and bacterial communities of fungus gardens in the fruit-tree pinhole borer, Xyleborinus saxesenii, from field and laboratory nests over time. By amplicon sequencing of probed fungus gardens of both nest types at three development phases we showed an extreme reduction of diversity in both bacterial and fungal symbionts in laboratory nests. Furthermore, we observed a general transition from nutritional to non-beneficial fungal symbionts during beetle development. While one known nutritional mutualist, Raffaelea canadensis, was occurring more or less stable over time, the second mutualist R. sulphurea was dominating young nests and decreased in abundance at the expense of other secondary fungi. The quicker the succession proceeded, the slower offspring beetles developed, suggesting a negative role of these secondary symbionts. Finally, we found signs of transgenerational costs of late dispersal for daughters, possibly as early dispersers transmitted and started their own nests with less of the non-beneficial taxa. Future studies should focus on the functional roles of the few bacterial taxa that were present in both field and laboratory nests.

First experimental evidence for active farming in ambrosia beetles and strong heredity of garden microbiomes

Fungal cultivation is a defining feature for advanced agriculture in fungus-farming ants and termites. In a third supposedly fungus-farming group, wood-colonizing ambrosia beetles, an experimental proof for the effectiveness of beetle activity for selective promotion of their food fungi over others is lacking and farming has only been assumed based on observations of social and hygienic behaviours. Here, we experimentally removed mothers and their offspring from young nests of the fruit-tree pinhole borer, Xyleborinus saxesenii. By amplicon sequencing of bacterial and fungal communities of nests with and without beetles we could show that beetles are indeed able to actively shift symbiont communities. Although being consumed, the Raffaelea food fungi were more abundant when beetles were present while a weed fungus (Chaetomium sp.) as well as overall bacterial diversity were reduced in comparison to nests without beetles. Core symbiont communities were generally of low diversity and there were strong signs for vertical transmission not only for the cultivars, but also for secondary symbionts. Our findings verify the existence of active farming, even though the exact mechanisms underlying the selective promotion and/or suppression of symbionts need further investigation.

Oak Decline Syndrome in Korean Forests: History, Biology, and Prospects for Korean Oak Wilt

Oak decline syndrome has been observed in South Korea and Japan and variously referred to as Korean oak wilt (KOW) and Japanese oak wilt (JOW). We reviewed aspects of the historical occurrence of KOW, disease cycle, and its potential causes. KOW has been seen principally in Mongolian oak (Quercus mongolica Fisch. ex Ledeb.). The first occurrence of KOW was in 2004 in Seongnam, South Korea. KOW is associated with the fungus Raffaelea quercus-mongolicae, which is vectored by the ambrosia beetle Platypus koryoensis. In addition, it has been suggested that yeasts have evolved a symbiotic relationship with the vector without antagonism for the pathogenic fungus. The number of trees in Korea killed by KOW increased to about 331,000 in 2011, but then decreased to about 157,000 in 2019. We hypothesized that trees infected by R. quercus-mongolicae accumulate phenolic compounds in the sapwood and the vector (P. koryoensis) beetles then avoid these trees. Therefore, the number of hosts available for the beetle after a KOW outbreak decrease due to accumulation of phenolic compounds in the wood, although most oak trees survive outbreaks. Therefore, P. koryoensis beetles move longer distances after outbreaks to find susceptible host trees. Novel occurrence of KOW in Korea may be due to either (1) an increase in tree age (size) in Korean oak stands, for which the beetle has a known preference or (2) climate change, which may be increasing the number of weakened or stressed trees, for which P. koryoensis also shows a preference.

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.

Microbiome Associated with the Mycangia of Female and Male Adults of the Ambrosia Beetle Platypus cylindrus Fab. (Coleoptera: Curculionidae)

The ambrosia beetle Platypus cylindrus Fab. (Coleoptera: Curculionidae) is a major cork oak pest in Portugal. Female and male beetles have different roles in host tree colonization and are both equipped with prothoracic mycangia for fungal transportation. Despite a known beneficial role of bacteria in ambrosia beetles, information on bacterial composition associated with prothoracic mycangia structures is scarce. Bacterial community from mycangia of P. cylindrus male and female beetles collected from cork oak galleries was investigated by means of 16S metagenomics. Mycangia anatomical structure was also explored with histological techniques and X-ray computed microtomography to highlight evidence supporting biological sexual dimorphism. A bacterial community with highly diverse bacterial taxa with low abundances at the genus level was revealed. Lactobacillales, Leptotrichia, Neisseria, Rothia, and Sphingomonadaceae were significantly more abundant in males, while Acinetobacter, Chitinophagaceae, Enterobacteriaceae, Erwiniaceae, Microbacteriaceae, and Pseudoclavibacter were more abundant in females. Additionally, a core bacteriome of five genera was shared by both sexes. Histological examination revealed visible connections linking external and internal tissues in females, but none in males. Overall, these results provide the first insights into sexual differentiation for bacteria in a Platypodinae beetle species, identifying key patterns of bacteria distribution in the context of beetle ecology and functional behavior.

Microbial Biocontrol Strategies for Ambrosia Beetles and Their Associated Phytopathogenic Fungi

Ambrosia beetles and their symbiotic fungi are causing severe damage in natural and agro-ecosystems worldwide, threatening the productivity of several important tree crops such as avocado. Strategies aiming at mitigating their impact include the application of broad-spectrum agrochemicals and the incineration of diseased trees, but the increasing demand for environment-friendly strategies call for exploring biological control for the management of ambrosia beetles and their phytopathogenic fungal symbionts. The aim of this review is to examine the existing knowledge on biocontrol approaches using beneficial microorganisms and microbial natural products with entomopathogenic and antifungal activity against ambrosia beetles and fungi. We show that biocontrol has been mainly focused on the insect, using entomopathogenic fungi (EPF) such as Beauveria spp. or Metarhizium spp. However, recent studies have been integrating EPF with mycoparasitic fungi such as Trichoderma spp. to simultaneously challenge the vector and its fungal symbionts. Novel approaches also include the use of microbial natural products as insect lures or antifungal agents. Contrastingly, the potential of bacteria, including actinobacteria (actinomycetes), as biocontrol agents of ambrosia fungi has been little investigated. We thus suggest that future research should further examine the antifungal activity of bacterial strains, with an emphasis on harsh environments. We also suggest pursuing the isolation of more effective microbial strains with dual biocontrol effect, i.e., exhibiting fungicidal/insecticidal activities. Moreover, additional efforts should aim at determining the best application methods of biocontrol agents in the field to ensure that the positive effects detected in vitro are sustained. Finally, we propose the integration of microbiome studies in pest and disease management strategies as they could provide us with tools to steer the beneficial host plant microbiome and to manipulate the beetle microbiome in order to reduce insect fitness.

Unique Attributes of the Laurel Wilt Fungal Pathogen, Raffaelea lauricola, as Revealed by Metabolic Profiling

Raffaelea lauricola is the causative agent of laurel wilt, a devastating disease of lauraceous trees. R. lauricola is also an obligate nutritional symbiont of several ambrosia beetle species who act as vectors for the pathogen. Here, we sought to establish the baseline “phenome” of R. lauricola with knowledge concerning its metabolic capability, expanding our understanding of how these processes are impacted by environmental and host nutrients. Phenotypic screening using a microarray of over one thousand compounds was used to generate a detailed profile of R. lauricola substrate utilization and chemical sensitivity. These data revealed (i) relatively restricted carbon utilization, (ii) broad sulfur and phosphate utilization, and (iii) pH and osmotic sensitivities that could be rescued by specific compounds. Additional growth profiling on fatty acids revealed toxicity on C10 substrates and lower, with robust growth on C12–C18 fatty acids. Conditions for lipid droplet (LD) visualization and LD dynamics were examined using a series of lipid dyes. These data provide unique insights regarding R. lauricola metabolism and physiology, and identify distinct patterns of substrate usage and sensitivity which likely reflect important aspects of the host-microbe interface and can be exploited for the development of strategies for mitigating the spread of laurel wilt.

Fungal mutualisms and pathosystems: life and death in the ambrosia beetle mycangia

Ambrosia beetles and their microbial communities, housed in specialized structures termed mycangia, represent one of the oldest and most diverse systems of mutualism and parasitism described thus far. Comprised of core filamentous fungal members, but also including bacteria and yeasts, the mycangia represent a unique adaptation that allows beetles to store and transport their source of nutrition. Although perhaps the most ancient of "farmers," the nature of these interactions remains largely understudied, with the exception of a handful of emerging pathosystems, where the fungal partner acts as a potentially devastating tree pathogen. Such virulence is often seen during "invasions," where (invasive) beetles carrying the fungal symbiont/plant pathogen expand into new territories and presumably "naïve" trees. Here, we summarize recent findings on the phylogenetic relationships between beetles and their symbionts and advances in the developmental and genetic characterization of the mechanisms that underlie insect-fungal-plant interactions. Results on genomic, transcriptomic, and metabolomic aspects of these relationships are described. Although many members of the fungal Raffaelea-beetle symbiont genera are relatively harmless to host trees, specialized pathosystems including wilt diseases of laurel and oak, caused by specific subspecies (R. lauricola and R. quercus, in the USA and East Asia, respectively), have emerged as potent plant pathogens capable of killing healthy trees. With the development of genetic tools, coupled to biochemical and microscopic techniques, the ambrosia beetle-fungal symbiont is establishing itself as a unique model system to study the molecular determinants and mechanisms that underlie the convergences of symbioses, mutualism, parasitism, and virulence. KEY POINTS: • Fungal-beetle symbioses are diverse and ancient examples of microbial farming. • The mycangium is a specialized structure on insects that houses microbial symbionts. • Some beetle symbiotic fungi are potent plant pathogens vectored by the insect.

A New Perspective of Pseudomonas-Host Interactions: Distribution and Potential Ecological Functions of the Genus Pseudomonas within the Bark Beetle Holobiont

Symbiosis between microbes and insects has been raised as a promising area for understanding biological implications of microbe-host interactions. Among them, the association between fungi and bark beetles has been generally recognized as essential for the bark beetle ecology. However, many works investigating bark beetle bacterial communities and their functions usually meet in a common finding: Pseudomonas is a broadly represented genus within this holobiont and it may provide beneficial roles to its host. Thus, we aimed to review available research on this microbe-host interaction and point out the probable relevance of Pseudomonas strains for these insects, in order to guide future research toward a deeper analysis of the importance of these bacteria for the beetle's life cycle.