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

Wood fibers are a crucial microhabitat for cellulose- and xylan- degrading bacteria in the hindgut of the wood-feeding beetle Odontotaenius disjunctus

Introduction

Wood digestion in insects relies on the maintenance of a mosaic of numerous microhabitats, each colonized by distinct microbiomes. Understanding the division of digestive labor between these microhabitats- is central to understanding the physiology and evolution of symbiotic wood digestion. A microhabitat that has emerged to be of direct relevance to the process of lignocellulose digestion is the surface of ingested plant material. Wood particles in the guts of some termites are colonized by a specialized bacterial fiber-digesting microbiome, but whether this represents a widespread strategy among insect lineages that have independently evolved wood-feeding remains an open question.

Methods

In this study, we investigated the bacterial communities specifically associated with wood fibers in the gut of the passalid beetle Odontotaenius disjunctus. We developed a Percoll-based centrifugation method to isolate and enrich the wood particles from the anterior hindgut, allowing us to access the wood fibers and their associated microbiome. We then performed assays of enzyme activity and used short-read and long-read amplicon sequencing of the 16S rRNA gene to identify the composition of the fiber-associated microbiome.

Results

Our assays demonstrated that the anterior hindgut, which houses a majority of the bacterial load, is an important site for lignocellulose digestion. Wood particles enriched from the anterior hindgut contribute to a large proportion of the total enzyme activity. The sequencing revealed that O. disjunctus, like termites, harbors a distinct fiber-associated microbiome, but notably, its community is enriched in insect-specific groups of Lactococcus and Turicibacter.

Discussion

Our study underscores the importance of microhabitats in fostering the complex symbiotic relationships between wood-feeding insects and their microbiomes. The discovery of distinct fiber-digesting symbionts in O. disjunctus, compared to termites, highlights the diverse evolutionary paths insects have taken to adapt to a challenging diet.

How feedback loops between meso- and macrofauna and organic residues contrasting in chemical quality determine decomposition dynamics in soils

The concept of feedback loops between changes in chemical quality of decomposing organic residues and changes in faunal communities was employed in studying how such feedback loops, representing distinct ecological successional stages, determine decomposition dynamics in soils. A 52-week litterbag decomposition study was superimposed onto an 18-year long term field experiment. Four types of organic residues contrasting in chemical quality (i.e., nitrogen (N), lignin, polyphenols, cellulose) were incorporated into soil annually to assess decomposition and associated meso- and macrofauna communities. In the first 4 weeks after residue incorporation (loop #1), the abundances (densities) of both mesofauna and macrofauna were positively influenced by labile cellulose and N. The mesofauna Collembola and Acari contributed 70-100% and 0-30% to the decomposition, respectively, while the macrofauna beetles and flies contributed 20-90% and 10-66%, respectively. The abundances were highest under groundnut (high N, low lignin) ([1.35 and 0.85 individual number (g dry litter)^-1] for mesofauna and macrofauna, respectively). The presence of macrofauna at week 2 led to a mass loss (R² = 0.67**), indicating that macrofauna preceded mesofauna in degrading residue. In week 8 (transition of loop #2 to #3), only macrofauna (beetles dominated contributing 65%) played an important role in lignin decomposition (R² = 0.56**), resulting in a mass loss (R² = 0.52**). In week 52 (loop #4) macrofauna, ants (Formicidae) replaced beetles as the dominant decomposers showing a feedback reaction to availability of protected cellulose. The Formicidans contributed 94% to the decomposition and influenced losses of mass (R² = 0.36*) and N (R² = 0.78***). The feedback loop concept provides a more comprehensive "two-sided" view into decomposition, as regulated simultaneously by two factors, than earlier "one-sided" approaches to soil fauna-mediated decomposition.

Larvae of an invasive scarab increase greenhouse gas emissions from soils and recruit gut mycobiota involved in C and N transformations

Background

Soil-derived prokaryotic gut communities of the Japanese beetle Popillia japonica Newman (JB) larval gut include heterotrophic, ammonia-oxidizing, and methanogenic microbes potentially capable of promoting greenhouse gas (GHG) emissions. However, no research has directly explored GHG emissions or the eukaryotic microbiota associated with the larval gut of this invasive species. In particular, fungi are frequently associated with the insect gut where they produce digestive enzymes and aid in nutrient acquisition. Using a series of laboratory and field experiments, this study aimed to (1) assess the impact of JB larvae on soil GHG emissions; (2) characterize gut mycobiota associated with these larvae; and (3) examine how soil biological and physicochemical characteristics influence variation in both GHG emissions and the composition of larval gut mycobiota.

Methods

Manipulative laboratory experiments consisted of microcosms containing increasing densities of JB larvae alone or in clean (uninfested) soil. Field experiments included 10 locations across Indiana and Wisconsin where gas samples from soils, as well as JB and their associated soil were collected to analyze soil GHG emissions, and mycobiota (ITS survey), respectively.

Results

In laboratory trials, emission rates of CO₂, CH₄, and N₂O from infested soil were ≥ 6.3× higher per larva than emissions from JB larvae alone whereas CO₂ emission rates from soils previously infested by JB larvae were 1.3× higher than emissions from JB larvae alone. In the field, JB larval density was a significant predictor of CO₂ emissions from infested soils, and both CO₂ and CH₄ emissions were higher in previously infested soils. We found that geographic location had the greatest influence on variation in larval gut mycobiota, although the effects of compartment (i.e., soil, midgut and hindgut) were also significant. There was substantial overlap in the composition and prevalence of the core fungal mycobiota across compartments with prominent fungal taxa being associated with cellulose degradation and prokaryotic methane production/consumption. Soil physicochemical characteristics such as organic matter, cation exchange capacity, sand, and water holding capacity, were also correlated with both soil GHG emission, and fungal a-diversity within the JB larval gut. Conclusions: Results indicate JB larvae promote GHG emissions from the soil directly through metabolic activities, and indirectly by creating soil conditions that favor GHG-associated microbial activity. Fungal communities associated with the JB larval gut are primarily influenced by adaptation to local soils, with many prominent members of that consortium potentially contributing to C and N transformations capable of influencing GHG emissions from infested soil.

Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential

Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.

Fungal diversity notes 1512-1610: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 14th in the Fungal Diversity Notes series, wherein we report 98 taxa distributed in two phyla, seven classes, 26 orders and 50 families which are described and illustrated. Taxa in this study were collected from Australia, Brazil, Burkina Faso, Chile, China, Cyprus, Egypt, France, French Guiana, India, Indonesia, Italy, Laos, Mexico, Russia, Sri Lanka, Thailand, and Vietnam. There are 59 new taxa, 39 new hosts and new geographical distributions with one new combination. The 59 new species comprise Angustimassarina kunmingense, Asterina lopi, Asterina brigadeirensis, Bartalinia bidenticola, Bartalinia caryotae, Buellia pruinocalcarea, Coltricia insularis, Colletotrichum flexuosum, Colletotrichum thasutense, Coniochaeta caraganae, Coniothyrium yuccicola, Dematipyriforma aquatic, Dematipyriforma globispora, Dematipyriforma nilotica, Distoseptispora bambusicola, Fulvifomes jawadhuvensis, Fulvifomes malaiyanurensis, Fulvifomes thiruvannamalaiensis, Fusarium purpurea, Gerronema atrovirens, Gerronema flavum, Gerronema keralense, Gerronema kuruvense, Grammothele taiwanensis, Hongkongmyces changchunensis, Hypoxylon inaequale, Kirschsteiniothelia acutisporum, Kirschsteiniothelia crustaceum, Kirschsteiniothelia extensum, Kirschsteiniothelia septemseptatum, Kirschsteiniothelia spatiosum, Lecanora immersocalcarea, Lepiota subthailandica, Lindgomyces guizhouensis, Marthe asmius pallidoaurantiacus, Marasmius tangerinus, Neovaginatispora mangiferae, Pararamichloridium aquisubtropicum, Pestalotiopsis piraubensis, Phacidium chinaum, Phaeoisaria goiasensis, Phaeoseptum thailandicum, Pleurothecium aquisubtropicum, Pseudocercospora vernoniae, Pyrenophora verruculosa, Rhachomyces cruralis, Rhachomyces hyperommae, Rhachomyces magrinii, Rhachomyces platyprosophi, Rhizomarasmius cunninghamietorum, Skeletocutis cangshanensis, Skeletocutis subchrysella, Sporisorium anadelphiae-leptocomae, Tetraploa dashaoensis, Tomentella exiguelata, Tomentella fuscoaraneosa, Tricholomopsis lechatii, Vaginatispora flavispora and Wetmoreana blastidiocalcarea. The new combination is Torula sundara. The 39 new records on hosts and geographical distribution comprise Apiospora guiyangensis, Aplosporella artocarpi, Ascochyta medicaginicola, Astrocystis bambusicola, Athelia rolfsii, Bambusicola bambusae, Bipolaris luttrellii, Botryosphaeria dothidea, Chlorophyllum squamulosum, Colletotrichum aeschynomenes, Colletotrichum pandanicola, Coprinopsis cinerea, Corylicola italica, Curvularia alcornii, Curvularia senegalensis, Diaporthe foeniculina, Diaporthe longicolla, Diaporthe phaseolorum, Diatrypella quercina, Fusarium brachygibbosum, Helicoma aquaticum, Lepiota metulispora, Lepiota pongduadensis, Lepiota subvenenata, Melanconiella meridionalis, Monotosporella erecta, Nodulosphaeria digitalis, Palmiascoma gregariascomum, Periconia byssoides, Periconia cortaderiae, Pleopunctum ellipsoideum, Psilocybe keralensis, Scedosporium apiospermum, Scedosporium dehoogii, Scedosporium marina, Spegazzinia deightonii, Torula fici, Wiesneriomyces laurinus and Xylaria venosula. All these taxa are supported by morphological and multigene phylogenetic analyses. This article allows the researchers to publish fungal collections which are important for future studies. An updated, accurate and timely report of fungus-host and fungus-geography is important. We also provide an updated list of fungal taxa published in the previous fungal diversity notes. In this list, erroneous taxa and synonyms are marked and corrected accordingly.

Stage correlation of symbiotic bacterial community and function in the development of litchi bugs (Hemiptera: Tessaratomidae)

Bacterial symbionts of insects have been shown to play important roles in host fitness. However, little is known about the bacterial community of Tessaratoma papillosa which is one of the most destructive pests of the well-known fruits Litchi chinensis Sonn and Dimocarpus longan Lour in Oriental Region, especially in South-east Asia and adjacent areas. In this study, we surveyed the bacterial community diversity and dynamics of T. papillosa in all developmental stages with both culture-dependent and culture-independent methods by the third-generation sequencing technology. Five bacterial phyla were identified in seven developmental stages of T. papillosa. Proteobacteria was the dominant phylum and Pantoea was the dominant genus of T. papillosa. The results of alpha and beta diversity analyses showed that egg stage had the most complex bacterial community. Some of different developmental stages showed similarities, which were clustered into three phases: (1) egg stage, (2) early nymph stages (instars 1-3), and (3) late nymph stages (instars 4-5) and adult stage. Functional prediction indicated that the bacterial community played different roles in these three phases. Furthermore, 109 different bacterial strains were isolated and identified from various developmental stages. This study revealed the relationship between the symbiotic bacteria and the development of T. papillosa, and may thus contribute to the biological control techniques of T. papillosa in the future.

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.

Multiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North America

Some insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these associations, and how these strategies relate to insect lifestyle, remains underexplored. We assessed subsocial passalid beetles of the species Odontotaenius disjunctus, and their frass (fecal material), which is an important food resource within their galleries, as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus frass collected across eastern North America harbored multiple lineages of Streptomyces and diverse antimicrobials. Metabolites detected in frass displayed synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. These findings support a model in which the lifestyle of O. disjunctus accommodates multiple Streptomyces lineages in their frass, resulting in a rich repertoire of antimicrobials that likely insulates their galleries against pathogenic invasion.

An Insight into Diversity and Functionalities of Gut Microbiota in Insects

The gut microbiota has long been of research interests due to its nutritional importance for many insects. It has been demonstrated that diversity of gut microbiota in insects can be modulated by many factors, including habitats, feeding preference, etc. Besides, the community structure of gut microbiota could also be altered during the different life stages of host insects. With development of conventional culture-dependent technologies and advanced culture-independent technologies, comprehensive and deep understanding of the functions of gut microbiota and their relationship with host insects were achieved, especially for the nutrient metabolic process mediated by them. In this review, we summarized the gut microbiota composition, major methods for gut microbiota characterization, and vital nutrient metabolic process mediated by gut microbiota in different insects. The increasing knowledge on the modulation of gut microbiota will help us for the comprehension of the contribution of gut microbiota to the nutritional metabolism of insects, prompting their growth and health.

Pseudobactrodesmium (Dactylosporaceae, Eurotiomycetes, Fungi) a Novel Lignicolous Genus

During our ongoing surveys of fungi on submerged wood in the Greater Mekong Subregion, we collected two new species similar to Bactrodesmium longisporum. Pseudobactrodesmium gen. nov. is introduced to accommodate the new species, P. aquaticum, P. chiangmaiensis and B. longisporum is transferred to this genus. Fasciculate conidiophores, enteroblastic conidiogenous cells and subulate to fusiform, phragmoseptate conidia with a tapering apical cell and sheath characterize the genus. Pseudobactrodesmium aquaticum has longer conidia than P. chiangmaiensis. The placement of Pseudobactrodesmium in Dactylosporaceae (Eurotiomycetes) is a novel finding based on analyses of combined LSU, SSU, ITS and RPB2 sequence data. Our study reveals that Pseudobactrodesmium is likely to be a speciose genus with different species in streams around the world.

New insights into the systematics of Bactrodesmium and its allies and introducing new genera, species and morphological patterns in the Pleurotheciales and Savoryellales (Sordariomycetes)

The newly discovered systematic placement of Bactrodesmium abruptum, the lectotype species of the genus, prompted a re-evaluation of the traditionally broadly conceived genus Bactrodesmium. Fresh material, axenic cultures and new DNA sequence data of five gene regions of six species, i.e. B. abruptum, B. diversum, B. leptopus, B. obovatum, B. pallidum and B. spilomeum, were studied. Bactrodesmium is a strongly resolved lineage in the Savoryellales (Sordariomycetes), supported by Bayesian and Maximum Likelihood methods. The genus Bactrodesmium is emended and delimited to hyphomycetes characterised by sporodochial conidiomata, mononematous often fasciculate conidiophores, holoblastic conidiogenesis and acrogenous, solitary, dry, pigmented, transversely or rarely longitudinally septate conidia. The conidia are seceding rhexolytically, exhibiting multiple secession patterns. An identification key to 35 species accepted in Bactrodesmium is given, providing the most important diagnostic characters. Novel DNA sequence data of B. longisporum and B. stilboideum confirmed their placement in the Sclerococcales (Eurotiomycetes). For other Bactrodesmium, molecular data are available for B. cubense and B. gabretae, which position them in the Dothideomycetes and Leotiomycetes, respectively. All four species are excluded from Bactrodesmium and segregated into new genera, Aphanodesmium, Gamsomyces and Kaseifertia. Classification of 20 other species and varieties not recognised in the genus is discussed. Based on new collections of Dematiosporium aquaticum, the type species of Dematiosporium, the genus is emended to accommodate monodictys-like freshwater lignicolous fungi of the Savoryellales characterised by effuse colonies, holoblastic conidiogenous cells and dictyosporous, pigmented conidia with a pore in each cell. Study of additional new collections, cultures and DNA sequence data revealed several unknown species, which are proposed as taxonomic novelties in the Savoryellales and closely related Pleurotheciales. Ascotaiwania latericolla, Helicoascotaiwania lacustris and Pleurotheciella erumpens are described from terrestrial, lentic and lotic habitats from New Zealand and France, respectively. New combinations are proposed for Helicoascotaiwania farinosa and Neoascotaiwania fusiformis. Relationships and systematics of the Savoryellales are discussed in the light of recent phylogenies and morphological patterns newly linked with the order through cultural studies.

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.

The influence of diet and environment on the gut microbial community of field crickets

The extent to which diet and environment influence gut community membership (presence or absence of taxa) and structure (individual taxon abundance) is the subject of growing interest in microbiome research. Here, we examined the gut bacterial communities of three cricket groups: (1) wild caught field crickets, (2) laboratory-reared crickets fed cat chow, and (3) laboratory-reared crickets fed chemically defined diets. We found that both environment and diet greatly altered the structure of the gut bacterial community. Wild crickets had greater gut microbial diversity and higher Firmicutes to Bacteroidetes ratios, in contrast to laboratory-reared crickets. Predictive metagenomes revealed that laboratory-reared crickets were significantly enriched in amino acid degradation pathways, while wild crickets had a higher relative abundance of peptidases that would aid in amino acid release. Although wild and laboratory animals differ greatly in their bacterial communities, we show that the community proportional membership remains stable from Phylum to Family taxonomic levels regardless of differences in environment and diet, suggesting that endogenous factors, such as host genetics, have greater control in shaping gut community membership.

Isolation of Fungi and Bacteria Associated with the Guts of Tropical Wood-Feeding Coleoptera and Determination of Their Lignocellulolytic Activities

The guts of beetle larvae constitute a complex system where relationships among fungi, bacteria, and the insect host occur. In this study, we collected larvae of five families of wood-feeding Coleoptera in tropical forests of Costa Rica, isolated fungi and bacteria from their intestinal tracts, and determined the presence of five different pathways for lignocellulolytic activity. The fungal isolates were assigned to three phyla, 16 orders, 24 families, and 40 genera; Trichoderma was the most abundant genus, detected in all insect families and at all sites. The bacterial isolates were assigned to five phyla, 13 orders, 22 families, and 35 genera; Bacillus, Serratia, and Pseudomonas were the dominant genera, present in all the Coleopteran families. Positive results for activities related to degradation of wood components were determined in 65% and 48% of the fungal and bacterial genera, respectively. Our results showed that both the fungal and bacterial populations were highly diverse in terms of number of species and their phylogenetic composition, although the structure of the microbial communities varied with insect host family and the surrounding environment. The recurrent identification of some lignocellulolytic-positive inhabitants suggests that particular microbial groups play important roles in providing nutritional needs for the Coleopteran host.