Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system

Biorefinery and Bioremediation Strategies for Efficient Management of Recalcitrant Pollutants Using Termites as an Obscure yet Promising Source of Bacterial Gut Symbionts: A Review

Lignocellulosic biomass (LCB) in the form of agricultural, forestry, and agro-industrial wastes is globally generated in large volumes every year. The chemical components of LCB render them a substrate valuable for biofuel production. It is hard to dissolve LCB resources for biofuel production because the lignin, cellulose, and hemicellulose parts stick together rigidly. This makes the structure complex, hierarchical, and resistant. Owing to these restrictions, the junk production of LCB waste has recently become a significant worldwide environmental problem resulting from inefficient disposal techniques and increased persistence. In addition, burning LCB waste, such as paddy straws, is a widespread practice that causes considerable air pollution and endangers the environment and human existence. Besides environmental pollution from LCB waste, increasing industrialization has resulted in the production of billions of tons of dyeing wastewater from several industries, including textiles, pharmaceuticals, tanneries, and food processing units. The massive use of synthetic dyes in various industries can be detrimental to the environment due to the recalcitrant aromatic structure of synthetic dyes, similar to the polymeric phenol lignin in LCB structure, and their persistent color. Synthetic dyes have been described as possessing carcinogenic and toxic properties that could be harmful to public health. Environmental pollution emanating from LCB wastes and dyeing wastewater is of great concern and should be carefully handled to mitigate its catastrophic effects. An effective strategy to curtail these problems is to learn from analogous systems in nature, such as termites, where woody lignocellulose is digested by wood-feeding termites and humus-recalcitrant aromatic compounds are decomposed by soil-feeding termites. The termite gut system acts as a unique bioresource consisting of distinct bacterial species valued for the processing of lignocellulosic materials and the degradation of synthetic dyes, which can be integrated into modern biorefineries for processing LCB waste and bioremediation applications for the treatment of dyeing wastewaters to help resolve environmental issues arising from LCB waste and dyeing wastewaters. This review paper provides a new strategy for efficient management of recalcitrant pollutants by exploring the potential application of termite gut bacteria in biorefinery and bioremediation processing.

Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut

BACKGROUND

The microbial landscape within termite guts varies across termite families. The gut microbiota of lower termites (LT) is dominated by cellulolytic flagellates that sequester wood particles in their digestive vacuoles, whereas in the flagellate-free higher termites (HT), cellulolytic activity has been attributed to fiber-associated bacteria. However, little is known about the role of individual lineages in fiber digestion, particularly in LT.

RESULTS

We investigated the lignocellulolytic potential of 2223 metagenome-assembled genomes (MAGs) recovered from the gut metagenomes of 51 termite species. In the flagellate-dependent LT, cellulolytic enzymes are restricted to MAGs of Bacteroidota (Dysgonomonadaceae, Tannerellaceae, Bacteroidaceae, Azobacteroidaceae) and Spirochaetota (Breznakiellaceae) and reflect a specialization on cellodextrins, whereas their hemicellulolytic arsenal features activities on xylans and diverse heteropolymers. By contrast, the MAGs derived from flagellate-free HT possess a comprehensive arsenal of exo- and endoglucanases that resembles that of termite gut flagellates, underlining that Fibrobacterota and Spirochaetota occupy the cellulolytic niche that became vacant after the loss of the flagellates. Furthermore, we detected directly or indirectly oxygen-dependent enzymes that oxidize cellulose or modify lignin in MAGs of Pseudomonadota (Burkholderiales, Pseudomonadales) and Actinomycetota (Actinomycetales, Mycobacteriales), representing lineages located at the hindgut wall.

CONCLUSIONS

The results of this study refine our concept of symbiotic digestion of lignocellulose in termite guts, emphasizing the differential roles of specific bacterial lineages in both flagellate-dependent and flagellate-independent breakdown of cellulose and hemicelluloses, as well as a so far unappreciated role of oxygen in the depolymerization of plant fiber and lignin in the microoxic periphery during gut passage in HT. Video Abstract.

Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems

The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.

Termite Microbial Symbiosis as a Model for Innovative Design of Lignocellulosic Future Biorefinery: Current Paradigms and Future Perspectives

The hunt for renewable and alternative fuels has driven research towards the biological conversion of lignocellulosic biomass (LCB) into biofuels, including bioethanol and biohydrogen. Among the natural biomass utilization systems (NBUS), termites represent a unique and easy-to-access model system to study host–microbe interactions towards lignocellulose bioconversion/valorization. Termites have gained significant interest due to their highly efficient lignocellulolytic systems. The wood-feeding termites apply a unique and stepwise process for the hydrolysis of lignin, hemicellulose, and cellulose via biocatalytic processes; therefore, mimicking their digestive metabolism and physiochemical gut environments might lay the foundation for an innovative design of nature-inspired biotechnology. This review highlights the gut system of termites, particularly the wood-feeding species, as a unique model for future biorefinery. The gut system of termites is a treasure-trove for prospecting novel microbial species, including protists, bacteria, and fungi, having higher biocatalytic efficiencies and biotechnological potentials. The significance of potential bacteria and fungi for harnessing the enzymes appropriate for lignocellulosic biorefinery is also discussed. Termite digestomes are rich sources of lignocellulases and related enzymes that could be utilized in various industrial processes and biomass-related applications. Consideration of the host and symbiont as a single functioning unit will be one of the most crucial strategies to expedite developments in termite-modeled biotechnology in the future.

Weight and protozoa number but not bacteria diversity are associated with successful pair formation of dealates in the Formosan subterranean termite, Coptotermes formosanus

New colonies of Formosan subterranean termites are founded by monogamous pairs. During swarming season, alates (winged reproductives) leave their parental colony. After swarming, they drop to the ground, shed their wings, and male and female dealates find suitable nesting sites where they mate and become kings and queens of new colonies. The first generation of offspring is entirely dependent on the nutritional resources of the founder pair consisting of the fat and protein reserves of the dealates and their microbiota, which include the cellulose-digesting protozoa and diverse bacteria. Since termite kings and queens can live for decades, mate for life and colony success is linked to those initial resources, we hypothesized that gut microbiota of founders affect pair formation. To test this hypothesis, we collected pairs found in nest chambers and single male and female dealates from four swarm populations. The association of three factors (pairing status, sex of the dealates and population) with dealate weights, total protozoa, and protozoa Pseudotrichonympha grassii numbers in dealate hindguts was determined. In addition, Illumina 16S rRNA gene sequencing and the QIIME2 pipeline were used to determine the impact of those three factors on gut bacteria diversity of dealates. Here we report that pairing status was significantly affected by weight and total protozoa numbers, but not by P. grassii numbers and bacteria diversity. Weight and total protozoa numbers were higher in paired compared to single dealates. Males contained significantly higher P. grassii numbers and bacteria richness and marginally higher phylogenetic diversity despite having lower weights than females. In conclusion, this study showed that dealates with high body weight and protozoa numbers are more likely to pair and become colony founders, probably because of competitive advantage. The combined nutritional resources provided by body weight and protozoa symbionts of the parents are important for successful colony foundation and development.

Exploring the region-wise diversity and functions of symbiotic bacteria in the gut system of wood-feeding termite, Coptotermes formosanus, toward the degradation of cellulose, hemicellulose, and organic dyes

The wood-feeding termite Coptotermes formosanus represents a unique and impressive system for lignocellulose degradation. The highly efficient digestion of lignocellulose is achieved through symbiosis with gut symbionts like bacteria. Despite extensive research during the last three decades, diversity of bacterial symbionts residing in individual gut regions of the termite and their associated functions is still lacking. To this end, cellulose, xylan, and dye-decolorization bacteria residing in foregut, midgut, and hindgut regions of C. formosanus were enlisted by using enrichment and culture-dependent molecular methods. A total of 87 bacterial strains were successfully isolated from different gut regions of C. formosanus which belonged to 27 different species of 10 genera, majorly affiliated with Proteobacteria (80%) and Firmicutes (18.3%). Among the gut regions, 37.9% of the total bacterial isolates were observed in the hindgut that demonstrated predominance of cellulolytic bacteria (47.6%). The majority of the xylanolytic and dye-decolorization bacteria (50%) were obtained from the foregut and midgut, respectively. Actinobacteria represented by Dietza sp. was observed in the hindgut only. Based on species richness, the highest diversity was observed in midgut and hindgut regions each of which harbored seven unique bacterial species. The members of Enterobacter, Klebsiella, and Pseudomonas were common among the gut regions. The lignocellulolytic activities of the selected potential bacteria signpost their assistance to the host for lignocellulose digestion. The overall results indicate that C. formosanus harbors diverse communities of lignocellulolytic bacteria in different regions of the gut system. These observations will significantly advance our understanding of the termite-bacteria symbiosis and their microbial ecology uniquely existed in different gut regions of C. formosanus, which may further shed a light on its potential values at termite-modeled biotechnology.

RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (Litopenaeus vannamei) in Different Stages of Development

White leg shrimp (Litopenaeus vannamei) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of L. vannamei has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of L. vannamei. In this study the metatranscriptome in different developmental stages of L. vannamei (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the Proteobacteria, Firmicutes and Actinobacteria, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in L. vannamei and the microbiome were shown. This study provides evidence of the interaction of the microbiome with L. vannamei, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of L. vannamei.

Phylogenetic identification of symbiotic protists of five Chinese Reticulitermes species indicates a cospeciation of gut microfauna with host termites

Symbiotic protists play important roles in the wood digestion of lower termites. Previous studies showed that termites generally possess host-specific flagellate communities. The genus Reticulitermes is particularly interesting because its unique assemblage of gut flagellates bears evidence for transfaunation. The gut fauna of Reticulitermes species in Japan, Europe, and North America had been investigated, but data on species in China are scarce. For the first time, we analyzed the phylogeny of protists in the hindgut of five Reticulitermes species in China. A total of 22 protist phylotypes were affiliated with the family Trichonymphidae, Teranymphidae, Trichomonadidae, and Holomastigotoididae (Phylum Parabasalia), and 45 protist phylotypes were affiliated with the family Pyrsonymphidae (Phylum Preaxostyla). The protist fauna of these five Reticulitermes species is similar to those of Reticulitermes species in other geographical regions. The topology of Trichonymphidae subtree was similar to that of Reticulitermes tree. All Preaxostyla clones were affiliated with the genera Pyrsonympha and Dinenympha (Order Oxymonadida) as in the other Reticulitermes species. The results of this study not only add to the existing information on the flagellates present in other Reticulitermes species but also offer the opportunity to test the hypotheses for the coevolution of symbiotic protists with their host termites.

Collaborative Response of the Host and Symbiotic Lignocellulytic System to Non-Lethal Toxic Stress in Coptotermes formosanus Skiraki

Simple Summary

Coptotermes formosanus Shiraki is a wood feeding lower termite and is widely distributed in many areas. The dynamic adjustment of the C. formosanus digestive system to unfavorable survival environments was investigated via non-lethal toxic feeding. The toxic stress did not change the dominant role of microbial lignocellulases in cellulose degradation of C. formosanus. The core symbiotic community was stable in abundance during the tolerance to the toxic treatment. However, a large number of low abundance taxa were significantly enriched by the low toxic feeding. These rare bacterial lineages likely contribute to toxic stress tolerance of termite. Above all, these findings add important new knowledge to our understanding of environmental adaptation of the lignocellulose hydrolysis system in termites.

Abstract

Disturbing the lignocellulose digestive system of termites is considered to be a promising approach for termite control. The research on the tolerance mechanism of the termite lignocellulose digestive system to harmful environment conditions is limited. In this study, we keep Coptotermes formosanus Skiraki under a non-lethal toxic condition by feeding the termites with filter paper containing the kojic acid (a low toxic insecticide). The effects of low toxic stress on the activities and gene expressions of host/symbiotic originated lignocellulases, and on the symbiotic microbial community structure of C. formosanus were explored. Our result showed that the low toxic stress would lead to the synchronous decrease of cellulase and hemicellulase activities, and supplementary increase of corresponding gene expressions. The symbiotic community maintained its role as the main force in the lignocellulolytic system of C. formosanus. Meanwhile, a large number of rare taxa were significantly enriched by kojic acid treatment. These numerically inconspicuous bacterial populations might be responsible for the functions similar to phenoloxidase or insecticide detoxification and enable C. formosanus to tolerate the harmful environment. Overall, our data suggested that the digestive adaptation of C. formosanus to physiotoxic feeding is closely related to the triple collaboration of termites–flagellates–bacteria.

Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review

Uprising fossil fuel depletion and deterioration of ecological reserves supply have led to the search for alternative renewable and sustainable energy sources and chemicals. Although first generation biorefinery is quite successful commercially in generating bulk of biofuels globally, the food versus fuel debate has necessitated the use of non-edible feedstocks, majorly waste biomass, for second generation production of biofuels and chemicals. A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB) and consolidated way of processing remains challenging. There were lot of research efforts in the past decade to scour for potential microbial candidate. In this context, evolution has developed the gut microbiota of several insects and ruminants that are potential LCB degraders host eco-system to overcome its host nutritional constraints, where LCB processed by microbiomes pretends to be a promising candidate. Synergistic microbial symbionts could make a significant contribution towards recycling the renewable carbon from distinctly abundant recalcitrant LCB. Several studies have assessed the bioprospection of innumerable gut symbionts and their lignocellulolytic enzymes for LCB degradation. Though, some reviews exist on molecular characterization of gut microbes, but none of them has enlightened the microbial community design coupled with various LCB valorization which intensifies the microbial diversity in biofuels application. This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding the holistic microbial community dynamics. Special emphasis is placed on gut microbial role in LCB depolymerization strategies to lignocellulolytic enzymes production and its functional metagenomic data mining eventually generating the sugar platform for biofuels and renewable chemicals production.

Division of functional roles for termite gut protists revealed by single-cell transcriptomes

The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four protists species comprising the protist population in worldwide pest Coptotermes formosanus. Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the protists, Cononympha leidyi, actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.

Biofilm architecture: An emerging synthetic biology target

Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite

Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host's lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding "higher" termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.

Meta-Omics Tools in the World of Insect-Microorganism Interactions

Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.

Filling Voids in Subterranean Termite (Blattodea: Rhinotermitidae) Bait Stations With Soil or Clay Improves Preference and Performance

Subterranean termites often transport soil into bait stations. In this study, we hypothesize that adding soil or clay material in the bait may affect preference and performance of termites. Choice and no-choice tests were conducted in the laboratory to investigate the aggregation and feeding preference, survivorship, wood consumption, and body water percentage of termites in response to food containers (here we simulated the bait station by placing a wood block into a bigger plastic box with termite-entering holes on the wall) with the void space filled with soil (sandy clay loam), clay material (sodium bentonite), or remained unfilled. Choice tests showed that under low-moisture conditions, food containers filled with clay attracted significantly more termites (Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) and Reticulitermes guangzhouensis Ping (Blattodea: Rhinotermitidae)) compared to food containers filled with soil, or unfilled. Under medium-moisture conditions, however, the percentages of termites that aggregated in the food containers filled with soil or clay were similar, and both were significant higher than the percentages in unfilled ones. In no-choice tests, the highest survivorship and wood consumption in C. formosanus were recorded under medium-moisture conditions and when food containers were filled with clay, whereas the lowest survivorship and wood consumption were recorded under low-moisture conditions and when food containers were filled with soil. Interestingly, presence of clay increased the body water percentage of termites. Our study enhances the understanding of the foraging ecology of subterranean termites, and may contribute to the improvement of termite-baiting technologies.

Symbiotic flagellate protists as cryptic drivers of adaptation and invasiveness of the subterranean termite Reticulitermes grassei Clément

Changes in flagellate protist communities of subterranean termite Reticulitermes grassei across different locations were evaluated following four predictions: (i) Rural endemic (Portugal mainland) termite populations will exhibit high diversity of symbionts; (ii) invasive urban populations (Horta city, Faial island, Azores), on the contrary, will exhibit lower diversity of symbionts, showing high similarity of symbiont assemblages through environmental filtering; (iii) recent historical colonization of isolated regions-as the case of islands-will imply a loss of symbiont diversity; and (iv) island isolation will trigger a change in colony breeding structure toward a less aggressive behavior. Symbiont flagellate protist communities were morphologically identified, and species richness and relative abundances, as well as biodiversity indices, were used to compare symbiotic communities in colonies from urban and rural environments and between island invasive and mainland endemic populations. To evaluate prediction on the impact of isolation (iv), aggression tests were performed among termites comprising island invasive and mainland endemic populations. A core group of flagellates and secondary facultative symbionts was identified. Termites from rural environments showed, in the majority of observed colonies, more diverse and abundant protist communities, probably confirming prediction (i). Corroborating prediction (ii), the two least diverse communities belong to termites captured inside urban areas. The Azorean invasive termite colonies had more diverse protist communities than expected and prediction (iii) which was not verified within this study. Termites from mainland populations showed a high level of aggressiveness between neighboring colonies, in contrast to the invasive colonies from Horta city, which were not aggressive to neighbors according to prediction (iv). The symbiotic flagellate community of R. grassei showed the ability to change in a way that might be consistent with adaptation to available conditions, possibly contributing to optimization of the colonization of new habitats and spreading of its distribution area, highlighting R. grassei potential as an invasive species.

NMR studies on lignocellulose deconstructions in the digestive system of the lower termite Coptotermes formosanus Shiraki

Termites represent one of the most efficient lignocellulose decomposers on earth. The mechanism by which termites overcome the recalcitrant lignin barrier to gain access to embedded polysaccharides for assimilation and energy remains largely unknown. In the present study, softwood, hardwood, and grass lignocellulose diets were fed to Coptotermes formosanus workers, and structural differences between the original lignocellulose diets and the resulting feces were examined by solution-state multidimensional nuclear magnetic resonance (NMR) techniques as well as by complementary wet-chemical methods. Overall, our data support the view that lignin polymers are partially decomposed during their passage through the termite gut digestive system, although polysaccharide decomposition clearly dominates the overall lignocellulose deconstruction process and the majority of lignin polymers remain intact in the digestive residues. High-resolution NMR structural data suggested preferential removal of syringyl aromatic units in hardwood lignins, but non-acylated guaiacyl units as well as tricin end-units in grass lignins. In addition, our data suggest that termites and/or their gut symbionts may favor degradation of C-C-bonded β-5 and resinol-type β-β lignin inter-monomeric units over degradation of ether-bonded β-O-4 units, which is in contrast to what has been observed in typical lignin biodegradation undertaken by wood-decaying fungi.

Effects of lignins as diet components on the physiological activities of a lower termite, Coptotermes formosanus Shiraki

We investigated the effects of lignins as diet components on the physiological activities of a lower termite, Coptotermes formosanus Shiraki. Artificial diets composed of polysaccharides with and without purified lignins (milled-wood lignins) from Japanese cedar (softwood), Japanese beech (hardwood), and rice (grass), were fed to C. formosanus workers. The survival and body mass of the workers as well as the presence of three symbiotic protists in the hindguts of the workers were then periodically examined. The survival rates of workers fed on diets containing lignins were, regardless of the lignocellulose diet sources, significantly higher than those of workers fed on only polysaccharides. In addition, it was clearly observed that all the tested lignins have positive effects on the maintenance of two major protists in the hindguts of C. formosanus workers, i.e., Pseudotrichonympha grassii and Holomastigotoides hartmanni. Overall, our data suggest that the presence of lignin is crucial to maintaining the physiological activities of C. formosanus workers during their lignocellulose decomposition. Our data also suggested that some components, possibly minerals and/or non-structural carbohydrates, in grass lignocellulose negatively affect the survival of C. formosanus workers as well as the present rate of the symbiotic protists in their hindguts.

Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome

Background

Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes. Nevertheless, several factors associated with the material sampling and library preparation steps make the metatranscriptomic studies of termite gut prokaryotic symbionts challenging.

Methods

In this study, we first examined the influence of the sampling strategy, including the whole termite gut and luminal fluid, on the diversity and the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. Secondly, we evaluated different commercially available kits combined in two library preparative pipelines for the best bacterial mRNA enrichment strategy.

Results

We showed that the sampling strategy did not significantly impact the generated results, both in terms of the representation of the microbes and their transcriptomic profiles. Nevertheless collecting luminal fluid reduces the co-amplification of unwanted RNA species of host origin. Furthermore, for the four studied higher termite species, the library preparative pipeline employing Ribo-Zero Gold rRNA Removal Kit “Epidemiology” in combination with Poly(A) Purist MAG kit resulted in a more efficient rRNA and poly-A-mRNAdepletion (up to 98.44% rRNA removed) than the pipeline utilizing MICROBExpress and MICROBEnrich kits. High correlation of both Ribo-Zero and MICROBExpresse depleted gene expression profiles with total non-depleted RNA-seq data has been shown for all studied samples, indicating no systematic skewing of the studied pipelines.

Conclusions

We have extensively evaluated the impact of the sampling strategy and library preparation steps on the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. The presented methodological approach has great potential to enhance metatranscriptomic studies of the higher termite intestinal flora and to unravel novel carbohydrate-active enzymes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4076-9) contains supplementary material, which is available to authorized users.

RNA interference unveils the importance of Pseudotrichonympha grassii cellobiohydrolase, a protozoan exoglucanase, in termite cellulose degradation

Based on prior work, a cellulase from glycosyl hydrolase family 7 (GHF7) was identified and found to be expressed at a high level in Coptotermes formosanus. To determine the function of GHF7 family members in vivo, we used RNA interference (RNAi) to functionally analyse the exoglucanase gene Pseudotrichonympha grassii cellobiohydrolase gene (PgCBH), which was highly expressed in Pseudotrichonympha grassii, a flagellate found in the hindgut of C. formosanus. In this study, the expression level of PgCBH was down-regulated by RNAi, causing the death of P. grassii, but no effect was observed for other flagellates found in C. formosanus. RNAi also resulted in significantly reduced exoglucanase activity, and no effect was observed for endoglucanase and β-glucosidase activities. This result demonstrated that the PgCBH gene plays a role in the protist lignocellulolytic process and is also important for host survival. PgCBH can be used as a target gene and has potential as a bioinsecticide for use against termites.

Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi

Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes). Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD) were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi. Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9) and beta-glucosidases (GH1) were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7) and endo-glucanases (GH5 and GH45), as well as classical xylanases (GH10 and GH11), were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi. Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs), which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.

Metatranscriptome of the protistan community in Reticulitermes flaviceps

The hindgut of lower termites harbors various symbiotic protists, which perform varied functions in lignocellulose decomposition. As termites are social insects, the species and numbers of these flagellated protists in the termite gut vary among the different castes. Juvenile hormones (JHs) can regulate caste differentiation in termites. In this study, we used the juvenile hormone analog fenoxycarb to induce termite workers (Reticulitermes flaviceps) to differentiate into pre-soldiers. A metatranscriptomic investigation of the protistan community was then performed by 454 pyrosequencing. From a thorough analysis based on 597 312 generated reads, we found that the starch and sucrose metabolism pathway was the most abundant pathway across the metatranscriptome. The current study demonstrates that the metatranscriptome of the protistan community in termites contains an abundance of lignocellulase, which plays a vital role in termite nutrition.

A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

Background

The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their evolutionary history often remains unexplored. One such protein is the small GTPase RABL2, recently implicated in the assembly of the sperm tail in mammals.

Results

Using the wealth of currently available genome and transcriptome sequences, including data from our on-going sequencing projects, we systematically analyzed the phylogenetic distribution and evolutionary history of RABL2 orthologs. Our dense taxonomic sampling revealed the presence of RABL2 genes in nearly all major eukaryotic lineages, including small “obscure” taxa such as breviates, ancyromonads, malawimonads, jakobids, picozoans, or palpitomonads. The phyletic pattern of RABL2 genes indicates that it was present already in the LECA. However, some organisms lack RABL2 as a result of secondary loss and our present sampling predicts well over 30 such independent events during the eukaryote evolution. The distribution of RABL2 genes correlates with the presence/absence of cilia: not a single well-established cilium-lacking species has retained a RABL2 ortholog. However, several ciliated taxa, most notably nematodes, some arthropods and platyhelminths, diplomonads, and ciliated subgroups of apicomplexans and embryophytes, lack RABL2 as well, suggesting some simplification in their cilium-associated functions. On the other hand, several algae currently unknown to form cilia, e.g., the “prasinophytes” of the genus Prasinoderma or the ochrophytes Pelagococcus subviridis and Pinguiococcus pyrenoidosus, turned out to encode not only RABL2, but also homologs of some hallmark ciliary proteins, suggesting the existence of a cryptic flagellated stage in their life cycles. We additionally obtained insights into the evolution of the RABL2 gene architecture, which seems to have ancestrally consisted of eight exons subsequently modified not only by lineage-specific intron loss and gain, but also by recurrent loss of the terminal exon encoding a poorly conserved C-terminal extension.

Conclusions

Our comparative analysis supports the notion that RABL2 is an ancestral component of the eukaryotic cilium and underscores the still underappreciated magnitude of recurrent gene loss, or reductive evolution in general, in the history of eukaryotic genomes and cells.

Reviewers

This article was reviewed by Berend Snel and James O. McInerney.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-016-0107-8) contains supplementary material, which is available to authorized users.

Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species

Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics.

Omic research in termites: an overview and a roadmap

Many recent breakthroughs in our understanding of termite biology have been facilitated by "omics" research. Omic science seeks to collectively catalog, quantify, and characterize pools of biological molecules that translate into structure, function, and life processes of an organism. Biological molecules in this context include genomic DNA, messenger RNA, proteins, and other biochemicals. Other permutations of omics that apply to termites include sociogenomics, which seeks to define social life in molecular terms (e.g., behavior, sociality, physiology, symbiosis, etc.) and digestomics, which seeks to define the collective pool of host and symbiont genes that collaborate to achieve high-efficiency lignocellulose digestion in the termite gut. This review covers a wide spectrum of termite omic studies from the past 15 years. Topics covered include a summary of terminology, the various kinds of omic efforts that have been undertaken, what has been revealed, and to a degree, what the results mean. Although recent omic efforts have contributed to a better understanding of many facets of termite and symbiont biology, and have created important new resources for many species, significant knowledge gaps still remain. Crossing these gaps can best be done by applying new omic resources within multi-dimensional (i.e., functional, translational, and applied) research programs.

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand

Stolotermes ruficeps is a widespread, primitive, lower termite occupying dead and decaying wood of many tree species in New Zealand's temperate forests. We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies. Most family and many genus-level taxa were common to S. ruficeps colonies despite being sampled from different tree species. Major taxa identified were Spirochaetaceae, Elusimicrobiaceae and Porphyromonadaceae. Others less well known in termite guts were Synergistaceae, Desulfobacteraceae, Rhodocyclaceae, Lachnospiraceae and Ruminococcaceae. Synergistaceae, Lachnospiraceae and Spirochaetaceae were well represented in the RNA data set, indicating a high-protein synthesis potential. Using 130,800 sequences from nine S. ruficeps DNA and RNA data sets, we estimated a high level of bacterial richness (4024 phylotypes at 3% genetic distance). Very few abundant phylotypes were site-specific; almost all (95%) abundant phylotypes, representing 97% of data set sequences, were detected in at least two S. ruficeps colonies. This study of a little-researched phylogenetically basal termite identifies core bacteria taxa. These findings will extend inventories of termite gut microbiota and contribute to the understanding of the specificity of termite gut microbiota.

Mining biomass-degrading genes through Illumina-based de novo sequencing and metagenomic analysis of free-living bacteria in the gut of the lower termite Coptotermes gestroi harvested in Vietnam

The 5.6 Gb metagenome of free-living microbial flora in the gut of the lower termite Coptotermes gestroi, harvested in Vietnam, was sequenced using Illumina technology. Genes related to biomass degradation were mined for a better understanding of biomass digestion in the termite gut and to identify lignocellulolytic enzymes applicable to biofuel production. The sequencing generated 5.4 Gb of useful reads, containing 125,431 ORFs spanning 78,271,365 bp, 80% of which was derived from bacteria. The 12 most abundant bacterial orders were Spirochaetales, Lactobacillales, Bacteroidales, Clostridiales, Enterobacteriales, Pseudomonades, Synergistales, Desulfovibrionales, Xanthomonadales, Burkholderiales, Bacillales, and Actinomycetales, and 1460 species were estimated. Of more than 12,000 ORFs with predicted functions related to carbohydrate metabolism, 587 encoding hydrolytic enzymes for cellulose, hemicellulose, and pectin were identified. Among them, 316 ORFs were related to cellulose degradation, and included β-glucosidases, 6-phospho-β-glucosidases, licheninases, glucan endo-1,3-β-D-glucosidases, endoglucanases, cellulose 1,4-β-cellobiosidases, glucan 1,3-β-glucosidases, and cellobiose phosphorylases. In addition, 259 ORFs were related to hemicellulose degradation, encoding endo-1,4-β-xylanases, α-galactosidases, α-N-arabinofuranosidases, xylan 1,4-β-xylosidases, arabinan endo-1,5-α-L-arabinosidases, endo-1,4-β-mannanases, and α-glucuronidases. Twelve ORFs encoding pectinesterases and pectate lyases were also obtained. To our knowledge, this is the first successful application of Illumina-based de novo sequencing for the analysis of a free-living bacterial community in the gut of a lower termite C. gestroi and for mining genes related to lignocellulose degradation from the gut bacteria.

Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle

BACKGROUND

Wood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, including cellulose and hemicellulose. Here, we present the midgut transcriptome of larval Anoplophora glabripennis, a wood-boring beetle with documented lignin-, cellulose-, and hemicellulose- degrading capabilities, which provides valuable insights into how this insect overcomes challenges associated with feeding in woody tissue.

RESULTS

Transcripts from putative protein coding regions of over 9,000 insect-derived genes were identified in the A. glabripennis midgut transcriptome using a combination of 454 shotgun and Illumina paired-end reads. The most highly-expressed genes predicted to encode digestive-related enzymes were trypsins, carboxylesterases, β-glucosidases, and cytochrome P450s. Furthermore, 180 unigenes predicted to encode glycoside hydrolases (GHs) were identified and included several GH 5, 45, and 48 cellulases, GH 1 xylanases, and GH 1 β-glucosidases. In addition, transcripts predicted to encode enzymes involved in detoxification were detected, including a substantial number of unigenes classified as cytochrome P450s (CYP6B) and carboxylesterases, which are hypothesized to play pivotal roles in detoxifying host tree defensive chemicals and could make important contributions to A. glabripennis' expansive host range. While a large diversity of insect-derived transcripts predicted to encode digestive and detoxification enzymes were detected, few transcripts predicted to encode enzymes required for lignin degradation or synthesis of essential nutrients were identified, suggesting that collaboration with microbial enzymes may be required for survival in woody tissue.

CONCLUSIONS

A. glabripennis produces a number of enzymes with putative roles in cell wall digestion, detoxification, and nutrient extraction, which likely contribute to its ability to thrive in a broad range of host trees. This system is quite different from the previously characterized termite fermentation system and provides new opportunities to discover enzymes that could be exploited for cellulosic ethanol biofuel production or the development of novel methods to control wood-boring pests.

Depletion of ribosomal RNA for mosquito gut metagenomic RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. Metagenomic RNA-Seq has become an important tool to analyze transcriptomes from various microbes present in a microbial community. Messenger RNA usually comprises only 1-3% of total RNA, while rRNA constitutes approximately 90%. It is challenging to enrich messenger RNA from a metagenomic microbial RNA sample because most prokaryotic mRNA species lack stable poly(A) tails. This prevents oligo d(T) mediated mRNA isolation. Here, we describe a protocol that employs sample derived rRNA capture probes to remove rRNA from a metagenomic total RNA sample. To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. Then, the community specific biotinylated antisense ribosomal RNA probes are synthesized in vitro using T7 RNA polymerase. The biotinylated rRNA probes are hybridized to the total RNA. The hybrids are captured by streptavidin-coated beads and removed from the total RNA. This subtraction-based protocol efficiently removes both mosquito and microbial rRNA from the total RNA sample. The mRNA enriched sample is further processed for RNA amplification and RNA-Seq.

Our second genome-human metagenome: how next-generation sequencer changes our life through microbiology

Next-generation sequencing has greatly expanded our ability to query the identity and genetic composition of entire communities of microbial organisms. This area of research, known as metagenomics, does not rely upon culturing the individual organisms. Rather, the genetic material from the entire community is processed and sequenced simultaneously. From this sequence data, researchers are able to determine the relative population of organisms within the community as well as determine which genes and metabolic pathways are present and expressed in the microbial community. While these techniques have been applied to a wide range of environmental samples, metagenomics is also the focus of intensive research on human-associated microbial communities. The scope of these human metagenomics studies are quite varied, but all have a common goal of attempting to understand the important role that human commensal microbial communities play in health and disease. The early results from studying the human metagenome indicate a vital role that microbial communities play in immunity, health, and disease. Going forward, human metagenomics is a wide open field of research with many unanswered questions such as which factors are responsible for the variation of composition of an individual's microbiome, how does the microbiome respond to disturbance, and what beneficial functions are the microorganisms performing?

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics.

Database URL:asgard.rc.fas.harvard.edu