Gut microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages

Microorganism Contribution to Mass-Reared Edible Insects: Opportunities and Challenges

The interest in edible insects' mass rearing has grown considerably in recent years, thereby highlighting the challenges of domesticating new animal species. Insects are being considered for use in the management of organic by-products from the agro-industry, synthetic by-products from the plastics industry including particular detoxification processes. The processes depend on the insect's digestive system which is based on two components: an enzymatic intrinsic cargo to the insect species and another extrinsic cargo provided by the microbial community colonizing-associated with the insect host. Advances have been made in the identification of the origin of the digestive functions observed in the midgut. It is now evident that the community of microorganisms can adapt, improve, and extend the insect's ability to digest and detoxify its food. Nevertheless, edible insect species such as Hermetia illucens and Tenebrio molitor are surprisingly autonomous, and no obligatory symbiosis with a microorganism has yet been uncovered for digestion. Conversely, the intestinal microbiota of a given species can take on different forms, which are largely influenced by the host's environment and diet. This flexibility offers the potential for the development of novel associations between insects and microorganisms, which could result in the creation of synergies that would optimize or expand value chains for agro-industrial by-products, as well as for contaminants.

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications

BACKGROUND

Gut microbiota have several advantages in influencing the host nutrition, metabolism, immunity and growth. However, the understanding of the gut microbiota in key edible wood-boring beetle larvae remain largely undefined. In the present study, the characteristics of the gut microbiota of two edible wood-boring species (Titocerus jaspideus and Passalus punctiger) from two indigenous forested areas were investigated.

RESULTS

Over 50% of Amplicon Sequence Variants (ASVs) constituted of Firmicutes in T. jaspideus. The dominant phyla in both beetle species were Bacteroidota (4.20-19.79%) and Proteobacteria (15.10-23.90%). Lactococcus lactis was the most abundant and core prokaryote in the guts of T. jaspideus. The fungi identified in the gut of both insects belong to the phylum Obazoa (66%) and Ascomycota (> 15%). Scheffersomyeces sp. was the core eukaryote recorded. The diversity of gut microbiota in both insect species did not vary significantly. Most of the prokaryotic genes expressed were predominantly associated with biosynthesis and metabolism.

CONCLUSION

Our findings demonstrated that Lactococcus lactis and Scheffersomyeces are core gut microbes of wood boring beetle larvae with desirable probiotic properties and promising use in food product fermentation for improved growth performance, gut barrier health, intestinal flora balance and immune protection for human and animals. Further studies to highlight the latest medical-based applications of L. lactis as live-delivery vector for the administration of therapeutics against both communicable and non-communicable diseases are warranted.

Uncovering the Antifungal Potential of Plant-Associated Cultivable Bacteria from the Aral Sea Region against Phytopathogenic Fungi

Two freshwater rivers, the Amu Darya and Syr Darya, flow into the Aral Sea, but they began to diminish in the early 1960s, and by the 1980s, the lake had nearly ceased to exist due to excessive water consumption for agriculture and the unsustainable management of water resources from rivers, which transformed the Aral Sea into a hypersaline lake. Despite this, the flora and fauna of the region began to evolve in the high-salinity seabed soil, which has received little attention in studies. In this study, we isolated approximately 1400 bacterial strains from the rhizosphere and phyllosphere of plant species of distinct families. Bacterial isolates were examined for antifungal activities against a range of pathogenic fungi such as Rhizoctonia gossypii, Trichothecium ovalisporum, Fusarium annulatum, F. oxysporum, F. culmorum, F. brachygibbosum, F. tricinctum, F. verticillioides, Alternaria alternata, A. terreus, Aspergillus niger, and As. flavus. Eighty-eight bacterial isolates exhibited varying antagonistic ability against pathogenic fungi. Furthermore, DNA barcoding of isolates using the 16S rRNA gene indicated that most antagonistic bacteria belonged to the Bacillus and Pseudomonas genera. The study also explored the activity of hydrolytic and cell-wall-degrading enzymes produced by antagonistic bacteria. The findings revealed that antagonistic bacteria can be utilized to widely protect seabed plants and plants growing in saline areas against pathogenic fungi, as well as agricultural crops.

Distinct metabolites affect the phloem fungal communities in ash trees (Fraxinus spp.) native and nonnative to the highly invasive emerald ash borer (AGRILUS PLANIPENNIS)

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co-evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co-evolution.

Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick)

Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.

Uncovering the antifungal activities of wild apple-associated bacteria against two canker-causing fungi, Cytospora mali and C. parasitica

Cytospora canker has become a devastating disease of apple species worldwide, and in severe cases, it may cause dieback of entire trees. The aim of this study was to characterize the diversity of cultivable bacteria from the wild apple microbiota and to determine their antifungal ability against the canker-causing pathogenic fungi Cytospora mali and C. parasitica. Five bacterial strains belonging to the species Bacillus amyloliquefaciens, B. atrophaeus, B. methylotrophicus, B. mojavensis, and Pseudomonas synxantha showed strong antagonistic effects against pathogenic fungi. Therefore, since the abovementioned Bacillus species produce known antifungal compounds, we characterized the antifungal compounds produced by Ps. synxantha. Bacteria grown on nutritional liquid medium were dehydrated, and the active compound from the crude extract was isolated and analysed via a range of chromatographic processes. High-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance analyses revealed a bioactive antifungal compound, phenazine-1-carboxylic acid (PCA). The minimum inhibitory concentration (MIC) demonstrated that PCA inhibited mycelial growth, with a MIC of 10 mg mL-1. The results suggested that PCA could be used as a potential compound to control C. mali and C. malicola, and it is a potential alternative for postharvest control of canker disease.

Emerald Ash Borer Management and Research: Decades of Damage and Still Expanding

Since the discovery of the ash tree (Fraxinus spp.) killer emerald ash borer (EAB; Agrilus planipennis) in the United States in 2002 and Moscow, Russia in 2003, substantial detection and management efforts have been applied to contain and monitor its spread and mitigate impacts. Despite these efforts, the pest continues to spread within North America. It has spread to European Russia and Ukraine and is causing sporadic outbreaks in its native range in China. The dynamics of EAB's range expansion events appear to be linked to the lack of resistant ash trees in invaded ranges, facilitated by the abundance of native or planted North American susceptible ash species. We review recently gained knowledge of the range expansion of EAB; its ecological, economic, and social impacts; and past management efforts with their successes and limitations. We also highlight advances in biological control, mechanisms of ash resistance, and new detection and management approaches under development, with the aim of guiding more effective management.

Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled

Bacteria of the Streptomyces genus constitute an authentic biotech gold mine thanks to their ability to produce a myriad of compounds and enzymes of great interest at various clinical, agricultural, and industrial levels. Understanding the physiology of these organisms and revealing their regulatory mechanisms is essential for their manipulation and application. Two-component systems (TCSs) constitute the predominant signal transduction mechanism in prokaryotes, and can detect a multitude of external and internal stimuli and trigger the appropriate cellular responses for adapting to diverse environmental conditions. These global regulatory systems usually coordinate various biological processes for the maintenance of homeostasis and proper cell function. Here, we review the multiple TCSs described and characterized in Streptomyces coelicolor, one of the most studied and important model species within this bacterial group. TCSs are involved in all cellular processes; hence, unravelling the complex regulatory network they form is essential for their potential biotechnological application.

Discovery of Rickettsia and Rickettsiella Intracellular Bacteria in Emerald Ash Borer Agrilus planipennis by Metagenomic Study of Larval Gut Microbiome in European Russia

Emerald ash borer Agrilus planipennis (Coleoptera: Buprestidae) is a quarantine pest posing a threat to ash trees all over Europe. This wood-boring beetle native to Asia is quickly spreading in North America and European Russia, and approaching the European Union and the Middle East. It is important to study microorganisms associated with this pest, because the knowledge of its “natural enemies” and “natural allies” could be potentially used for the control of the pest. All previously published information about the A. planipennis microbiome was obtained in North America and China. We present the first study on procaryotes associated with A. planipennis in Europe. Alive larvae were sampled from under the bark of Fraxinus pennsylvanica in the Moscow Oblast and the gut microbiome was studied using metagenomic methods. Next-generation Illumina-based amplicon sequencing of the v3-v4 region 16S-RNA gene was performed. In total, 439 operational taxonomic units from 39 families and five phyla were detected. The dominant families in our samples were Pseudomonadaceae, Erwiniaceae and Enterobacteriaceae, in accordance with the published information on the larval gut microbiome in North America and China. We detected intracellular bacteria in A. planipennis for the first time, namely Rickettsia (Rickettsiaceae) and Rickettsiella (Diplorickettsiaceae). Representatives of the genus Rickettsia are known to be in mutualistic symbiosis with some phytophagous insects, while Rickettsiella bacteria are pathogenic to many arthropods. The finding of Rickettsia and Rickettsiella opens perspectives for future research on the interactions between these bacteria and A. planipennis and the possible use of these interactions for the control of the pest.

Comparative Nanopore Sequencing-Based Evaluation of the Midgut Microbiota of the Summer Chafer (Amphimallon solstitiale L.) Associated with Possible Resistance to Entomopathogenic Nematodes

Root-feeding Amphimallon solstitiale larvae and certain other scarab beetles are the main soil-dwelling pests found in Europe, while entomopathogenic nematodes (EPN) have been used as a biocontrol agent against these species. Our study provides the first detailed characterization of the bacterial community of the midgut in wild A. solstitiale larvae, based on the nanopore sequencing of the 16S rRNA gene. In the whole dataset, we detected 2586 different genera and 11,641 species, with only 83 diverse bacterial genera shared by all studied individuals, which may represent members of the core midgut microbiota of A. solstitiale larvae. Subsequently, we compared the midgut microbiota of EPN-resistant and T0 (prior to EPN exposure) individuals, hypothesizing that resistance to this parasitic infection may be linked to the altered gut community. Compared to the control, the resistant insect microbiota demonstrated lower Shannon and Evenness indices and significant differences in the community structure. Our studies confirmed that the gut microbiota alternation is associated with resistant insects; however, there are many processes involved that can affect the bacterial community. Further research on the role of gut microbiota in insect-parasitic nematode interaction may ultimately lead to the improvement of biological control strategies in insect pest management.

Screening and Molecular Identification of Bacteria from the Midgut of Amphimallon solstitiale Larvae Exhibiting Antagonistic Activity against Bacterial Symbionts of Entomopathogenic Nematodes

Entomopathogenic nematodes (Rhabditida: Steinernematidae and Heterorhabditidae) are a group of organisms capable of infecting larvae of insects living in soil, including representatives of the family Scarabaeidae. Their insecticidal activity is related to the presence of symbiotic bacteria Xenorhabdus spp. or Photorhabdus spp. in the alimentary tract, which are released into the insect body, leading to its death caused by bacterial toxins and septicemia. Although the antibacterial activities of symbionts of entomopathogenic nematodes have been well described, there is insufficient knowledge of the interactions between these bacteria and microorganisms that naturally inhabit the alimentary tract of insects infested by nematodes. In this study, 900 bacterial strains isolated from midgut samples of Amphimallon solstitiale larvae were tested for their antagonistic activity against the selected five Xenorhabdus and Photorhabdus species. Cross-streak tests showed significant antibacterial activity of 20 isolates. These bacteria were identified as Bacillus [Brevibacterium] frigoritolerans, Bacillus toyonensis, Bacillus wiedmannii, Chryseobacterium lathyri, Chryseobacterium sp., Citrobacter murliniae, Enterococcus malodoratus, Paenibacillus sp., Serratia marcescens and Serratia sp. Since some representatives of the intestinal microbiota of A. solstitiale are able to inhibit the growth of Xenorhabdus and Photorhrhabdus bacteria in vitro, it can be assumed that this type of bacterial interaction may occur at certain stages of insect infection by Steinernema or Heterorhabditis nematodes.

Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus mali in Tianshan Forests

The gut microflora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of the gut bacteria to address this absence of fungi in the larval gut. The results demonstrated that the gut bacteria were able to selectively inhibit wild apple tree-associated fungi. Among them, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC, and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identified. Activity of the compound was determined by the minimum inhibitory concentration method and electron microscopy. Moreover, our study showed that the gut bacteria could originate from noninfested apple microflora during infestation. Overall, the results showed that in newly invaded locations, A. mali larvae changed their gut microbiota and adopted new gut bacteria that prevented fungal colonization in the gut.

The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

The microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

Fungi associated with galleries of the emerald ash borer

The emerald ash borer (EAB) is an exotic forest pest that has killed millions of ash trees in the United States and Canada, resulting in an ecological disaster and billions of dollars in economic losses of urban landscape and forest trees. The beetle was first detected in Michigan in 2002 and has spread through much of the Eastern and Midwestern U.S., reaching Minnesota in 2009. Since then, it has spread across the state and poses a great risk to the more than 1 billion ash trees in Minnesota. The larval stage of EAB creates wounds on trees as they feed on the inner bark, causing disruption of water and sap flow that results in tree death. The fungal community associated with EAB larval galleries is poorly understood and the role these fungi may play in tree death is not known. This study describes fungi isolated from EAB larval galleries sampled throughout the main geographic areas of Minnesota where ash is affected by EAB. Fungal cultures were identified by extracting genomic DNA and sequencing the ITS region of the rDNA. Results from 1126 isolates reveal a diverse assemblage of fungi and three functional guilds comprised of canker pathogens, wood decay, and entomopathogenic fungi. The most common canker-associated genera were Cytospora followed by Phaeoacremonium, Paraconiothyrium, Coniothyrium, Nectria, Diplodia, and Botryosphaeria. Fungi in the Basidiomycota were nearly all wood decay causing fungi and many were species of pioneer colonizing genera including Sistotrema, Irpex, Peniophora, Phlebia and Ganoderma. Some of these fungi seriously affect urban trees, having the potential to cause rapid wood decay resulting in hazardous tree situations. Several entomopathogenic genera with the potential for biological control of EAB were also isolated from galleries. Purpureocillium was the most commonly isolated genus, followed by Beauveria, Clonostachys, Lecanicillium, Akanthomyces, Cordyceps, Microcera, Tolypocladium, and Pochonia. The results identify important fungal functional guilds that are occupying a new niche in ash trees resulting from EAB and include fungi that may accelerate decline in tree health, increase hazard tree situations, or may provide options for biological control of this destructive invasive insect.

Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges

The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.

Bacterial community profile after the lethal infection of Steinernema-Xenorhabdus pairs into soil-reared Tenebrio molitor larvae

The host microbiota may have an impact on pathogens. This is often studied in laboratory-reared hosts but rarely in individuals whose microbiota looks like that of wild animals. In this study, we modified the gut microbiota of the insect Tenebrio molitor by rearing larvae in soil sampled from the field. We showed by high throughput sequencing methods that this treatment modifies the gut microbiota so that it is more diversified than that of laboratory-reared insects, and closely resembled the one of soil-dwelling insects. To describe what the entomopathogenic bacterial symbiont Xenorhabdus (Enterobacteriaceae), vectored by the soil-dwelling nematode Steinernema, might experience in natural conditions, we studied the infestation of the soil-reared T. molitor larvae with three Steinernema-Xenorhabdus pairs. We performed the infestation at 18°C, which delays the emergence of new infective juveniles (IJs), the soil-dwelling nematode forms, but which is a temperature compatible with natural infestation. We analyzed by high throughput sequencing methods the composition of the bacterial community within the insect cadavers before the first emergences of IJs. These bacterial communities were generally characterized by one or two non-symbiont taxa. Even for highly lethal Steinernema-Xenorhabdus pairs, the symbiont does not dominate the bacterial community within the insect cadaver.

Why do entomologists and plant pathologists approach trophic relationships so differently? Identifying biological distinctions to foster synthesis

Plant interactions with herbivores and pathogens are among the most widespread ecological relationships, and show many congruent properties. Despite these similarities, general models describing how plant defenses function in ecosystems, and the prioritization of responses to emerging challenges such as climate change, invasive species and habitat alteration, often differ markedly between entomologists and plant pathologists. We posit that some fundamental distinctions between how insects and pathogens interact with plants underlie these differences. We propose a conceptual framework to help incorporate these distinctions into robust models and research priorities. The most salient distinctions include features of host-searching behavior, evasion of plant defenses, plant tolerance to utilization, and sources of insect and microbial population regulation. Collectively, these features lead to relatively more diffuse and environmentally mediated plant-insect interactions, and more intimate and genetically driven plant-pathogen interactions. Specific features of insect vs pathogen life histories can also yield different patterns of spatiotemporal dynamics. These differences can become increasingly pronounced when scaling from controlled laboratory to open ecological systems. Integrating these differences alongside similarities can foster improved models and research approaches to plant defense, trophic interactions, coevolutionary dynamics, food security and resource management, and provide guidance as traditional departments increase collaborations, or merge into larger units.

Characterization of the gut microbiota of invasive Agrilus mali Matsumara (Coleoptera: Buprestidae) using high-throughput sequencing: uncovering plant cell-wall degrading bacteria

The genus Agrilus comprises diverse exotic and agriculturally important wood-boring insects that have evolved efficient digestive systems. Agrilus mali Matsumara, an invasive insect, is causing extensive mortality to endangered wild apple trees in Tianshan. In this study, we present an in-depth characterization of the gut microbiota of A. mali based on high-throughput sequencing of the 16S rRNA gene and report the presence of lignocellulose-degrading bacteria. Thirty-nine operational taxonomic units (OTUs) were characterized from the larval gut. OTUs represented 6 phyla, 10 classes, 16 orders, 20 families, and 20 genera. The majority of bacterial OTUs belonged to the order Enterobacteriales which was the most abundant taxa in the larval gut. Cultivable bacteria revealed 9 OTUs that all belonged to Gammaproteobacteria. Subsequently, we examined the breakdown of plant cell-wall compounds by bacterial isolates. Among the isolates, the highest efficiency was observed in Pantoea sp., which was able to synthesize four out of the six enzymes (cellulase, cellobiase, β-xylanase, and β-gluconase) responsible for plant-cell wall degradation. One isolate identified as Pseudomonas orientalis exhibited lignin peroxidase activity. Our study provides the first characterization of the gut microbial diversity of A. mali larvae and shows that some cultivable bacteria play a significant role in the digestive tracts of larvae by providing nutritional needs.

Diversity of Bacterial Biota in Capnodis tenebrionis (Coleoptera: Buprestidae) Larvae

The bacterial biota in larvae of Capnodis tenebrionis, a serious pest of cultivated stone-fruit trees in the West Palearctic, was revealed for the first time using the MiSeq platform. The core bacterial community remained the same in neonates whether upon hatching or grown on peach plants or an artificial diet, suggesting that C. tenebrionis larvae acquire much of their bacterial biome from the parent adult. Reads affiliated with class levels Gammaproteobacteria and Alphaproteobacteria (phylum Proteobacteria ca. 86%), and Actinobacteria (ca. 14%) were highly abundant. Most diverse reads belong to the families Xanthomonadaceae (50%), Methylobacteriaceae (20%), Hyphomicrobiaceae (9%), Micrococcaceae (7%) and Geodermatophilaceae (4.5%). About two-thirds of the reads are affiliated with the genera Lysobacter, Microvirga, Methylobacterium, and Arthrobacter, which encompass species displaying cellulolytic and lipolytic activities. This study provides a foundation for future studies to elucidate the roles of bacterial biota in C. tenebrionis.

Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results

BACKGROUND

Glossina pallidipes is a haematophagous insect that serves as a cyclic transmitter of trypanosomes causing African Trypanosomiasis (AT). To fully assess the role of G. pallidipes in the epidemiology of AT, especially the human form of the disease (HAT), it is essential to know the microbial diversity inhabiting the gut of natural fly populations. This study aimed to examine the diversity of G. pallidipes fly gut bacteria by culture-dependent approaches.

RESULTS

113 bacterial isolates were obtained from aerobic and anaerobic microorganisms originating from the gut of G. pallidipes. 16S rDNA of each isolate was PCR amplified and sequenced. The overall majority of identified bacteria belonged in descending order to the Firmicutes (86.6%), Actinobacteria (7.6%), Proteobacteria (5.5%)and Bacteroidetes (0.3%). Diversity of Firmicutes was found higher when enrichments and isolation were performed under anaerobic conditions than aerobic ones. Experiments conducted in the absence of oxygen (anaerobiosis) led to the isolation of bacteria pertaining to four phyla (83% Firmicutes, 15% Actinobacteria, 1% Proteobacteria and 0.5% Bacteroidetes, whereas those conducted in the presence of oxygen (aerobiosis) led to the isolation of bacteria affiliated to two phyla only (90% Firmicutes and 10% Proteobacteria). Phylogenetic analyses placed these isolates into 11 genera namely Bacillus, Acinetobacter, Mesorhizobium, Paracoccus, Microbacterium, Micrococcus, Arthrobacter, Corynobacterium, Curtobacterium, Vagococcus and Dietzia spp.which are known to be either facultative anaerobes, aerobes, or even microaerobes.

CONCLUSION

This study shows that G. pallidipes fly gut is an environmental reservoir for a vast number of bacterial species, which are likely to be important for ecological microbial well being of the fly and possibly on differing vectorial competence and refractoriness against AT epidemiology.

Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions

The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.

High diversity and variability in the bacterial microbiota of the coffee berry borer (Coleoptera: Curculionidae), with emphasis on Wolbachia

AIMS

Variation in microbiota of the coffee berry borer (CBB) Hypothenemus hampei was studied. Diversity, structure and function of bacterial communities were compared between eggs vs adults, CBBs from shade coffee vs sun coffee, CBBs from the field vs raised in the laboratory, and CBBs with and without the antibiotic tetracycline.

METHODS AND RESULTS

We sequenced the region V4 of the gene 16 S rRNA. Pseudomonadaceae and Enterobacteriaceae, particularly Pseudomonas and Pantoea, dominated microbiotas of the CBB. Comparative functional inferences with PICRUSt suggested that samples from the field were enriched for genes involved in carbohydrate and protein digestion and absorption, while laboratory-reared samples were higher in genes for melanization and caffeine metabolism.

CONCLUSIONS

Microbiotas of the CBB were diverse and dominated by the genus Pseudomonas, several species of which have been previously associated with caffeine degradation in this insect. Wolbachia was the only endosymbiont detected with known ability to manipulate host reproduction.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that stage of development and origin of samples affected the structure and function of the CBB's bacterial communities. This is the first attempt to predict functional significance of the CBB microbiota in nutrition, reproduction and defence.

Bacterial Symbionts in Lepidoptera: Their Diversity, Transmission, and Impact on the Host

The insect’s microbiota is well acknowledged as a “hidden” player influencing essential insect traits. The gut microbiome of butterflies and moths (Lepidoptera) has been shown to be highly variable between and within species, resulting in a controversy on the functional relevance of gut microbes in this insect order. Here, we aim to (i) review current knowledge on the composition of gut microbial communities across Lepidoptera and (ii) elucidate the drivers of the variability in the lepidopteran gut microbiome and provide an overview on (iii) routes of transfer and (iv) the putative functions of microbes in Lepidoptera. To find out whether Lepidopterans possess a core gut microbiome, we compared studies of the microbiome from 30 lepidopteran species. Gut bacteria of the Enterobacteriaceae, Bacillaceae, and Pseudomonadaceae families were the most widespread across species, with Pseudomonas, Bacillus, Staphylococcus, Enterobacter, and Enterococcus being the most common genera. Several studies indicate that habitat, food plant, and age of the host insect can greatly impact the gut microbiome, which contributes to digestion, detoxification, or defense against natural enemies. We mainly focus on the gut microbiome, but we also include some examples of intracellular endosymbionts. These symbionts are present across a broad range of insect taxa and are known to exert different effects on their host, mostly including nutrition and reproductive manipulation. Only two intracellular bacteria genera (Wolbachia and Spiroplasma) have been reported to colonize reproductive tissues of Lepidoptera, affecting their host’s reproduction. We explore routes of transmission of both gut microbiota and intracellular symbionts and have found that these microbes may be horizontally transmitted through the host plant, but also vertically via the egg stage. More detailed knowledge about the functions and plasticity of the microbiome in Lepidoptera may provide novel leads for the control of lepidopteran pest species.

Contaminants of emerging concern affect Trichoplusia ni growth and development on artificial diets and a key host plant

Many countries are utilizing reclaimed wastewater for agriculture because drought, rising temperatures, and expanding human populations are increasing water demands. Unfortunately, wastewater often contains biologically active, pseudopersistent pharmaceuticals, even after treatment. Runoff from farms and output from wastewater treatment plants also contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on an agricultural pest, Trichoplusia ni (Lepidoptera: Noctuidae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Trichoplusia ni showed increased developmental time and mortality when reared on artificial diets containing antibiotics, hormones, or a mixture of contaminants. Mortality was also increased when T. ni were reared on tomatoes grown hydroponically with the same concentrations of antibiotics. The antibiotic-treated plants translocated ciprofloxacin through their tissues to roots, shoots, and leaves. Microbial communities of T. ni changed substantially between developmental stages and when exposed to CECs in their diets. Our results suggest that use of reclaimed wastewater for irrigation of crops can affect the developmental biology and microbial communities of an insect of agricultural importance.

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community

Drought, rising temperatures, and expanding human populations are increasing water demands. Many countries are extending potable water supplies by irrigating crops with wastewater. Unfortunately, wastewater contains biologically active, long-lived pharmaceuticals, even after treatment. Run-off from farms and wastewater treatment plant overflows contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on a cosmopolitan saprophagous insect, Megaselia scalaris (Diptera: Phoridae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Female flies showed no oviposition preference for treated or untreated diets. Larvae exposed to caffeine in diets showed increased mortality, and larvae fed antibiotics and hormones showed signs of slowed development, especially in females. The normal sex ratio observed in M. scalaris from control diets was affected by exposure to caffeine and pharmaceutical mixture treatments. There was an overall effect of treatment on the flies’ microbial communities; notably, caffeine fed insects displayed higher microbial variability. Eight bacterial families accounted for approximately 95% of the total microbes in diet and insects. Our results suggest that CECs at environmentally relevant concentrations can affect the biology and microbial communities of an insect of ecological and medical importance.

Bacteriome-Localized Intracellular Symbionts in Pollen-Feeding Beetles of the Genus Dasytes (Coleoptera, Dasytidae)

Several insect taxa are associated with intracellular symbionts that provision limiting nutrients to their hosts. Such tightly integrated symbioses are especially common in insects feeding on nutritionally challenging diets like phloem sap or vertebrate blood, but also occur in seed-eating and omnivorous taxa. Here, we characterize an intracellular symbiosis in pollen-feeding beetles of the genus Dasytes (Coleoptera, Dasytidae). High-throughput tag-encoded 16S amplicon pyrosequencing of adult D. plumbeus and D. virens revealed a single gamma-proteobacterial symbiont ('Candidatus Dasytiphilus stammeri') that amounts to 52.4-98.7% of the adult beetles' entire microbial community. Almost complete 16S rRNA sequences phylogenetically placed the symbiont into a clade comprising Buchnera and other insect endosymbionts, but sequence similarities to these closest relatives were surprisingly low (83.4-87.4%). Using histological examination, three-dimensional reconstructions, and fluorescence in situ hybridization, we localized the symbionts in three mulberry-shaped bacteriomes that are associated with the mid- to hind-gut transition in adult male and female beetles. Given the specialized pollen-feeding habits of the adults that contrasts with the larvae's carnivorous lifestyle, the symbionts may provision limiting essential amino acids or vitamins as in other intracellular symbioses, or they might produce digestive enzymes that break up the fastidious pollen walls and thereby contribute to the host's nutrition. In either case, the presence of gamma-proteobacterial symbionts in pollen-feeding beetles indicates that intracellular mutualists are more widely distributed across insects with diverse feeding habits than previously recognized.

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.

Bacterial Community Diversity Harboured by Interacting Species

All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

Microbial Diversity in the Gut of Cashew Stem Girdler, Analeptes trifasciata Fabricius (Coleoptera: Cerambycidae), in Ibadan, Nigeria

The cashew stem girdler, Analeptes trifasciata, is a major insect pest of cashew in Nigeria causing economic damage in cashew plantations even at low density. In this study, newly emerged adults of A. trifasciata reared from field-infested cashew stems were collected from the rearing cages, sexed, and dissected to reveal the internal structures of the insects. The gut was excised and separated into the foregut, midgut, and hindgut. The dissected gut compartments were blotted dry by sandwiching in sterile Whatman No. 1 (150 mm) filter paper for a minute. The inoculated gut parts showed the presence of eight fungi flora, namely, Aspergillus repens, Trichoderma spp., Fusarium verticillioides, Lasiodiplodia theobromae, yeast, Aspergillus niger, Fusarium spp., and Rhizopus stolonifer. The frequencies of occurrence of bacteria in the gut compartments of A. trifasciata were Enterobacter spp.: 83.33%; Escherichia coli and Streptococcus spp.: 55.56% each; Staphylococcus spp.: 44.44%; Klebsiella pneumonia: 50% and Salmonella shigella: 11.11%, while each of Serratia marceascea, Pseudomonas spp., and Micrococcus lutea had 5.56% occurrence. The occurrence of mycoflora and microbiota species varied in the gut compartments of A. trifasciata, indicating the role of these microorganisms in metabolic and other bioprocesses of A. trifasciata during digestion and synthesis of complex food substances from the cashew stem substrate. This study would provide basic information for enzymatic studies of A. trifasciata with a view to developing an integrated pest management (IPM) protocol for managing the pest in cashew plantations.

Taxonomy, Physiology, and Natural Products of Actinobacteria

Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota

Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species.

Characterization of actinobacteria associated with three ant-plant mutualisms

Ant-plant mutualisms are conspicuous and ecologically important components of tropical ecosystems that remain largely unexplored in terms of insect-associated microbial communities. Recent work has revealed that ants in some ant-plant systems cultivate fungi (Chaetothyriales) within their domatia, which are fed to larvae. Using Pseudomyrmex penetrator/Tachigali sp. from French Guiana and Petalomyrmex phylax/Leonardoxa africana and Crematogaster margaritae/Keetia hispida, both from Cameroon, as models, we tested the hypothesis that ant-plant-fungus mutualisms co-occur with culturable Actinobacteria. Using selective media, we isolated 861 putative Actinobacteria from the three systems. All C. margaritae/K. hispida samples had culturable Actinobacteria with a mean of 10.0 colony forming units (CFUs) per sample, while 26 % of P. penetrator/Tachigali samples (mean CFUs 1.3) and 67 % of P. phylax/L. africana samples (mean CFUs 3.6) yielded Actinobacteria. The largest number of CFUs was obtained from P. penetrator workers, P. phylax alates, and C. margaritae pupae. 16S rRNA gene sequencing and phylogenetic analysis revealed the presence of four main clades of Streptomyces and one clade of Nocardioides within these three ant-plant mutualisms. Streptomyces with antifungal properties were isolated from all three systems, suggesting that they could serve as protective symbionts, as found in other insects. In addition, a number of isolates from a clade of Streptomyces associated with P. phylax/L. africana and C. margaritae/K. hispida were capable of degrading cellulose, suggesting that Streptomyces in these systems may serve a nutritional role. Repeated isolation of particular clades of Actinobacteria from two geographically distant locations supports these isolates as residents in ant-plant-fungi niches.

Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles

Background

Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages.

Results

Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants.

Conclusions

The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles’ unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1096) contains supplementary material, which is available to authorized users.

Uncovering the cultivable microbial diversity of costa rican beetles and its ability to break down plant cell wall components

Coleopterans are the most diverse insect order described to date. These organisms have acquired an array of survival mechanisms through their evolution, including highly efficient digestive systems. Therefore, the coleopteran intestinal microbiota constitutes an important source of novel plant cell wall-degrading enzymes with potential biotechnological applications. We isolated and described the cultivable fungi, actinomycetes and aerobic eubacteria associated with the gut of larvae and adults from six different beetle families colonizing decomposing logs in protected Costa Rican ecosystems. We obtained 611 isolates and performed phylogenetic analyses using the ITS region (fungi) and 16S rDNA (bacteria). The majority of fungal isolates belonged to the order Hypocreales (26% of 169 total), while the majority of actinomycetes belonged to the genus Streptomyces (86% of 241 total). Finally, we isolated 201 bacteria spanning 19 different families belonging into four phyla: Firmicutes, α, β and γ-proteobacteria. Subsequently, we focused on microbes isolated from Passalid beetles to test their ability to degrade plant cell wall polymers. Highest scores in these assays were achieved by a fungal isolate (Anthostomella sp.), two Streptomyces and one Bacillus bacterial isolates. Our study demonstrates that Costa Rican beetles harbor several types of cultivable microbes, some of which may be involved in symbiotic relationships that enable the insect to digest complex polymers such as lignocellulose.

Large shift in symbiont assemblage in the invasive red turpentine beetle

Changes in symbiont assemblages can affect the success and impact of invasive species, and may provide knowledge regarding the invasion histories of their vectors. Bark beetle symbioses are ideal systems to study changes in symbiont assemblages resulting from invasions. The red turpentine beetle (Dendroctonus valens) is a bark beetle species that recently invaded China from its native range in North America. It is associated with ophiostomatalean fungi in both locations, although the fungi have previously been well-surveyed only in China. We surveyed the ophiostomatalean fungi associated with D. valens in eastern and western North America, and identified the fungal species using multi-gene phylogenies. From the 307 collected isolates (147 in eastern North America and 160 in western North America), we identified 20 species: 11 in eastern North America and 13 in western North America. Four species were shared between eastern North America and western North America, one species (Ophiostoma floccosum) was shared between western North America and China, and three species (Grosmannia koreana, Leptographium procerum, and Ophiostoma abietinum) were shared between eastern North America and China. Ophiostoma floccosum and O. abietinum have worldwide distributions, and were rarely isolated from D. valens. However, G. koreana and L. procerum are primarily limited to Asia and North America respectively. Leptographium procerum, which is thought to be native to North America, represented >45% of the symbionts of D. valens in eastern North America and China, suggesting D. valens may have been introduced to China from eastern North America. These results are surprising, as previous population genetics studies on D. valens based on the cytochrome oxidase I gene have suggested that the insect was introduced into China from western North America.

Comparative evaluation of the gut microbiota associated with the below- and above-ground life stages (larvae and beetles) of the forest cockchafer, Melolontha hippocastani

A comparison of the diversity of bacterial communities in the larval midgut and adult gut of the European forest cockchafer (Melolontha hippocastani) was carried out using approaches that were both dependent on and independent of cultivation. Clone libraries of the 16S rRNA gene revealed 150 operational taxonomic units (OTUs) that belong to 11 taxonomical classes and two other groups that could be classified only to the phylum level. The most abundant classes were β, δ and γ-proteobacteria, Clostridia, Bacilli, Erysipelotrichi and Sphingobacteria. Although the insect’s gut is emptied in the prepupal stage and the beetle undergoes a long diapause period, a subset of eight taxonomic classes from the aforementioned eleven were found to be common in the guts of diapausing adults and the larval midguts (L2, L3). Moreover, several bacterial phylotypes belonging to these common bacterial classes were found to be shared by the larval midgut and the adult gut. Despite this, the adult gut bacterial community represented a subset of that found in the larvae midgut. Consequently, the midgut of the larval instars contains a more diverse bacterial community compared to the adult gut. On the other hand, after the bacteria present in the larvae were cultivated, eight bacterial species were isolated. Moreover, we found evidence of the active role of some of the bacterial species isolated in food digestion, namely, the presence of amylase and xylanolytic properties. Finally, fluorescence in situ hybridization allowed us to confirm the presence of selected species in the insect gut and through this, their ecological niche as well as the metagenomic results. The results presented here elucidated the heterogeneity of aerobic and facultative bacteria in the gut of a holometabolous insect species having two different feeding habits.

Gut microbiota in nymph and adults of the giant mesquite bug (Thasus neocalifornicus) (Heteroptera: Coreidae) is dominated by Burkholderia acquired de novo every generation

The coreid bug Thasus neocalifornicus Brailovsky and Barrera, commonly known as the giant mesquite bug, is a ubiquitous insect of the southwestern United States. Both nymphs and adults are often found aggregated on mesquite trees (Prosopis spp.: Fabaceae) feeding on seedpods and plant sap. We characterized the indigenous bacterial populations of nymphs and adults of this species by using molecular and phylogenetic techniques and culturing methods. Results show that this insect's bacterial gut community has a limited diversity dominated by Burkholderia associates. Phylogenetic analysis by using 16s rRNA sequences suggests that these β-Proteobacteria are closely related to those symbionts obtained from other heteropteran midgut microbial communities but not to Burkholderia symbionts associated with other insect orders. These bacteria were absent from the eggs and were not found in all younger nymphs, suggesting that they are acquired after the insects have hatched. Rearing experiments of nymphs with potentially Burkholderia contaminated soil suggested that if this symbiont is not acquired, giant mesquite bugs experience higher mortality. Egg, whole-body DNA extractions of younger nymphs, and midgut DNA extractions of fifth-instar nymphs and adults also revealed the presence of α-Proteobacteria from the Wolbachia genus. However, this bacterium was also present in reproductive organs of adults, indicating that this symbiont is not specific to the gut.

Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio

Sirex noctilio is an invasive wood-feeding wasp that threatens the world's commercial and natural pine forests. Successful tree colonization by this insect is contingent on the decline of host defenses and the ability to utilize the woody substrate as a source of energy. We explored its potential association with bacterial symbionts that may assist in nutrient acquisition via plant biomass deconstruction using growth assays, culture-dependent and -independent analysis of bacterial frequency of association and whole-genome analysis. We identified Streptomyces and γ-Proteobacteria that were each associated with 94% and 88% of wasps, respectively. Streptomyces isolates grew on all three cellulose substrates tested and across a range of pH 5.6 to 9. On the basis of whole-genome sequencing, three Streptomyces isolates have some of the highest proportions of genes predicted to encode for carbohydrate-active enzymes (CAZyme) of sequenced Actinobacteria. γ-Proteobacteria isolates grew on a cellulose derivative and a structurally diverse substrate, ammonia fiber explosion-treated corn stover, but not on microcrystalline cellulose. Analysis of the genome of a Pantoea isolate detected genes putatively encoding for CAZymes, the majority predicted to be active on hemicellulose and more simple sugars. We propose that a consortium of microorganisms, including the described bacteria and the fungal symbiont Amylostereum areolatum, has complementary functions for degrading woody substrates and that such degradation may assist in nutrient acquisition by S. noctilio, thus contributing to its ability to be established in forested habitats worldwide.

Antioxidant genes of the emerald ash borer (Agrilus planipennis): gene characterization and expression profiles

Phytophagous insects frequently encounter reactive oxygen species (ROS) from exogenous and endogenous sources. To overcome the effect of ROS, insects have evolved a suite of antioxidant defense genes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione peroxidase (GPX). The emerald ash borer (Agrilus planipennis Fairmaire), an exotic invasive insect pest from Asia has killed millions of ash trees and continues to invade North America at a rapid pace. From an on-going expressed sequence tag (EST) project of A. planipennis larval tissues, we identified ESTs coding for a Cu-Zn SOD (ApSOD1), a CAT (ApCAT1) and a GPX (ApGPX1). A multiple sequence alignment of the derived A. planipennis sequences revealed high homology with other insect sequences at the amino acid level. Phylogenetic analysis of ApSOD1 grouped it with Cu-Zn SODs of other insect taxa. Quantitative real time PCR (qRT-PCR) analysis in different larval tissues (midgut, fat body, Malpighian tubule and cuticle) revealed high mRNA levels of ApCAT1 in the midgut. Interestingly, high mRNA levels for both ApSOD1 and ApGPX1 were observed in the Malpighian tubules. Assay of mRNA levels in developmental stages (larva, prepupa and adults) by qRT-PCR indicated high transcript levels of ApCAT1 and ApGPX1 in larval and prepupal stages with a decline in adults. On the other hand, the transcript levels of ApSOD1 were observed to be constitutive in all the developmental stages assayed. Results obtained reflect a plausible role of these A. planipennis antioxidant genes in quenching ROS from both diet (ash allelochemicals) as well as endogenous sources. These studies further help in understanding the adaptation/invasiveness of A. planipennis.

From commensal to pathogen: translocation of Enterococcus faecalis from the midgut to the hemocoel of Manduca sexta

A dynamic homeostasis is maintained between the host and native bacteria of the gastrointestinal tract in animals, but migration of bacteria from the gut to other organs can lead to disease or death. Enterococcus faecalis is a commensal of the gastrointestinal tract; however, Enterococcus spp. are increasingly frequent causes of nosocomial infections with a high mortality rate. We investigated the commensal-to-pathogen switch undergone by E. faecalis OG1RF in the lepidopteran model host Manduca sexta associated with its location in the host. E. faecalis persists in the harsh midgut environment of M. sexta larvae without causing apparent illness, but injection of E. faecalis directly into the larval hemocoel is followed by rapid death. Additionally, oral ingestion of E. faecalis in the presence of Bacillus thuringiensis insecticidal toxin, a pore-forming toxin that targets the midgut epithelium, induces an elevated mortality rate. We show that the loss of gut integrity due to B. thuringiensis toxin correlates with the translocation of E. faecalis from the gastrointestinal tract into the hemolymph. Upon gaining access to the hemolymph, E. faecalis induces an innate immune response, illustrated by hemocyte aggregation, in larvae prior to death. The degree of hemocyte aggregation is dependent upon the route of E. faecalis entry. Our data demonstrate the efficacy of the M. sexta larval model system in investigating E. faecalis-induced sepsis and clarifies controversies in the field regarding the events leading to larval death following B. thuringiensis toxin exposure.

This study advances our knowledge of Enterococcus faecalis-induced sepsis following translocation from the gut and provides a model for mammalian diseases in which the spatial distribution of bacteria determines disease outcomes. We demonstrate that E. faecalis is a commensal in the gut of Manduca sexta and a pathogen in the hemocoel, resulting in a robust immune response and rapid death, a process we refer to as the “commensal-to-pathogen” switch. While controversy remains regarding Bacillus thuringiensis toxin-induced killing, our laboratory previously found that under some conditions, the midgut microbiota is essential for B. thuringiensis toxin killing of Lymantria dispar (N. A. Broderick, K. F. Raffa, and J. Handelsman, Proc. Natl. Acad. Sci. U. S. A. 103:15196–15199, 2006; B. Raymond, et al., Environ. Microbiol. 11:2556–2563, 2009; P. R. Johnston, and N. Crickmore, Appl. Environ. Microbiol. 75:5094–5099, 2009). We and others have demonstrated that the role of the midgut microbiota in B. thuringiensis toxin killing is dependent upon the lepidopteran species and formulation of B. thuringiensis toxin (N. A. Broderick, K. F. Raffa, and J. Handelsman, Proc. Natl. Acad. Sci. U. S. A. 103:15196–15199, 2006; N. A. Broderick, et al., BMC Biol. 7:11, 2009). This work reconciles much of the apparently contradictory previous data and reveals that the M. sexta-E. faecalis system provides a model for mammalian sepsis.

Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis)

BACKGROUND

The insect midgut and fat body represent major tissue interfaces that deal with several important physiological functions including digestion, detoxification and immune response. The emerald ash borer (Agrilus planipennis), is an exotic invasive insect pest that has killed millions of ash trees (Fraxinus spp.) primarily in the Midwestern United States and Ontario, Canada. However, despite its high impact status little knowledge exists for A. planipennis at the molecular level.

METHODOLOGY AND PRINCIPAL FINDINGS

Newer-generation Roche-454 pyrosequencing was used to obtain 126,185 reads for the midgut and 240,848 reads for the fat body, which were assembled into 25,173 and 37,661 high quality expressed sequence tags (ESTs) for the midgut and the fat body of A. planipennis larvae, respectively. Among these ESTs, 36% of the midgut and 38% of the fat body sequences showed similarity to proteins in the GenBank nr database. A high number of the midgut sequences contained chitin-binding peritrophin (248)and trypsin (98) domains; while the fat body sequences showed high occurrence of cytochrome P450s (85) and protein kinase (123) domains. Further, the midgut transcriptome of A. planipennis revealed putative microbial transcripts encoding for cell-wall degrading enzymes such as polygalacturonases and endoglucanases. A significant number of SNPs (137 in midgut and 347 in fat body) and microsatellite loci (317 in midgut and 571 in fat body) were predicted in the A. planipennis transcripts. An initial assessment of cytochrome P450s belonging to various CYP clades revealed distinct expression patterns at the tissue level.

CONCLUSIONS AND SIGNIFICANCE

To our knowledge this study is one of the first to illuminate tissue-specific gene expression in an invasive insect of high ecological and economic consequence. These findings will lay the foundation for future gene expression and functional studies in A. planipennis.

From structure to function: the ecology of host-associated microbial communities

In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

Microbiological study of bulls of indulgence of the 15th-16th centuries

During the restoration of the church of "San Esteban" in Cuéllar (Segovia, Spain) a few sepulchres were opened. Among them was that of Doña Isabel de Zuazo, from the 16th century. Together with the corpse was found a series of printed documents from the 15th-16th centuries, most of which were bulls of indulgence. A microbiological study of the documents was carried out using techniques of isolation and molecular microbiology, together with scanning electron microscopy. Most of the identified bacteria were highly suggestive of a human origin, particularly the predominance of Clostridium species consistent with the flora of the human intestinal tract. Our results demonstrate that appreciable post-mortem migration of bacteria has taken place from the corpse to the historic documents. This can be explained considering that the documents were found on pelvic region, and were contaminated by body fluids and putrefaction.

Complete genome sequence of Meiothermus silvanus type strain (VI-R2)

Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes

Fifteen million hectares of pine forests in western Canada have been attacked by the mountain pine beetle (Dendroctonus ponderosae; MPB), leading to devastating economic losses. Grosmannia clavigera and Leptographium longiclavatum, are two fungi intimately associated with the beetles, and are crucial components of the epidemic. To detect and discriminate these two closely related pathogens, we utilized a method based on ligase-mediated nucleotide discrimination with padlock probe technology, and signal amplification by hyperbranched rolling circle amplification (HRCA). Two padlock probes were designed to target species-specific single nucleotide polymorphisms (SNPs) located at the inter-generic spacer 2 region and large subunit of the rRNA respectively, which allows discrimination between the two species. Thirty-four strains of G. clavigera and twenty-five strains of L. longiclavatum representing a broad geographic origin were tested with this assay. The HRCA results were largely in agreement with the conventional identification based on morphology or DNA-based methods. Both probes can also efficiently distinguish the two MPB-associated fungi from other fungi in the MPB, as well as other related fungi in the order Ophiostomatales. We also tested this diagnostic method for the direct detection of these fungi from the DNA of MPB. A nested PCR approach was used to enrich amplicons for signal detection. The results confirmed the presence of these two fungi in MPB. Thus, the padlock probe assay coupled with HRCA is a rapid, sensitive and reproducible method for the identification and detection of these ophiostomatoid fungi.

Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia

Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.