Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes

Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates

Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.

The evolutionary adaptation of shrimp hemocyanin subtypes and the consequences on their structure and functions

Hemocyanin is the main respiratory protein of arthropods and is formed by hexameric and/or oligomeric subunits. Due to changes in the living environment and gene rearrangement, various hemocyanin subtypes and subunits evolved in crustaceans. This paper reviews the various hemocyanin subtypes and isoforms in shrimp and analyses published genomic data of sixteen hemocyanin family genes from Litopenaeus vannamei to explore the evolution of hemocyanin genes, subunits, and protein structure. Analysis of hemocyanin subtypes distribution and structure in various tissues was also performed and related to multiple and tissue-specific functions, i.e., immunological activity, immune signaling, phenoloxidase activity, modulation of microbiota homeostasis, and energy metabolism. The functional diversity of shrimp hemocyanin due to molecular polymorphism, transcriptional regulation, alternative splicing, degradation into functional peptides, interaction with other proteins or genes, and structural differences will also be highlighted for future research. Inferences would be drawn from other crustaceans to explain how evolution has changed the structure-function of hemocyanin and its implication for evolutionary research into the multifunctionality of hemocyanin and other related proteins in shrimp.

Individual level microbial communities in the digestive system of the freshwater isopod Asellus aquaticus: Complex, robust and prospective

The freshwater isopod Asellus aquaticus is an important decomposer of leaf detritus, and its diverse gut microbiome has been depicted as key contributors in lignocellulose degradation as of terrestrial isopods. However, it is not clear whether the individual-level microbiome profiles in the isopod digestive system across different habitats match the implied robust digestion function of the microbiome. Here, we described the bacterial diversity and abundance in the digestive system (hindgut and caeca) of multiple A. aquaticus individuals from two contrasting freshwater habitats. Individuals from a lake and a stream harboured distinct microbiomes, indicating a strong link between the host-associated microbiome and microbes inhabiting the environments. While faeces likely reflected the variations in environmental microbial communities included in the diet, the microbial communities also substantially differed in the hindgut and caeca. Microbes closely related to lignocellulose degradation are found consistently more enriched in the hindgut in each individual. Caeca often associated with taxa implicated in endosymbiotic/parasitic roles (Mycoplasmatales and Rickettsiales), highlighting a complex host-parasite-microbiome interaction. The results highlight the lability of the A. aquaticus microbiome supporting the different functions of the two digestive organs, which may confer particular advantages in freshwater environments characterized by seasonally fluctuating and spatially disparate resource availability.

Molecular insights into the evolution of woody plant decay in the gut of termites

Plant cell walls represent the most abundant pool of organic carbon in terrestrial ecosystems but are highly recalcitrant to utilization by microbes and herbivores owing to the physical and chemical barrier provided by lignin biopolymers. Termites are a paradigmatic example of an organism's having evolved the ability to substantially degrade lignified woody plants, yet atomic-scale characterization of lignin depolymerization by termites remains elusive. We report that the phylogenetically derived termite Nasutitermes sp. efficiently degrades lignin via substantial depletion of major interunit linkages and methoxyls by combining isotope-labeled feeding experiments and solution-state and solid-state nuclear magnetic resonance spectroscopy. Exploring the evolutionary origin of lignin depolymerization in termites, we reveal that the early-diverging woodroach Cryptocercus darwini has limited capability in degrading lignocellulose, leaving most polysaccharides intact. Conversely, the phylogenetically basal lineages of "lower" termites are able to disrupt the lignin-polysaccharide inter- and intramolecular bonding while leaving lignin largely intact. These findings advance knowledge on the elusive but efficient delignification in natural systems with implications for next-generation ligninolytic agents.

Prospection of putative genes for digestive enzymes based on functional genome of the hepatopancreas of Amazon river prawn

Over recent years, Macrobrachium amazonicum has become a popular species for shrimp farming due to their fast growth, high survival rates, and marketability. Several studies have focused on the development of new technology for the culture of this species, but many aspects of their nutrition and physiology remain unknown. Thus, the goal of the present study was to obtain transcripts of putative genes encoding digestive enzymes, based on a library of the cDNA from the hepatopancreas of M. amazonicum, sequenced in the Ion TorrentTM platform. We identified fragments of nine genes related to digestive enzymes, acting over proteins, carbohydrates and lipids. Endo and exoproteases were also recorded in the hepatopancreas, indicating adaptation to the digestion of protein-rich foods. Nonetheless, the enzymes involved in the carbohydrate metabolism formed the largest functional group in M. amazonicum, including enzymes related to the digestion of starch, chitin, and cellulose. These findings indicate that the species has a genetic apparatus of a well-adapted omnivorous animal. This information may provide important insights for the selection of ingredients for the formulation of a more appropriate diet to the enzymatic repertoire of M. amazonicum.

De novo transcriptome assembly of the midgut glands of herbivorous land crabs, Chiromantes haematocheir, and identification of laccase genes involved in lignin degradation

Herbivorous land crabs such as Chiromantes haematocheir and C. dehaani show biomass-degrading activities. In this study, we performed RNA-seq analysis to detect biomass-degrading enzymes. A de novo transcriptome assembly in the midgut glands of molting and non-molting C. haematocheir crabs was constructed using RNA sequencing. Illumina sequencing generated 44,937,002 and 44,394,310 reads from the two midgut glands. In total, 178,710 contigs with an average length of 750 bp and an N50 value of 1,235 bp were assembled, of which 37,890 contigs were annotated using BLASTx search against the NCBI database. We identified 22 contigs (11 genes) belonging to the laccase family and 44 contigs (22 genes) belonging to the peroxidase family. Sixteen contigs (three genes) belonging to the GH9 cellulase family were also detected. We selected the gene accounting for the majority of expressed laccase and analyzed its properties. The 24131-laccase transcript (2465 bp) had one complete open reading frame, nt 149-1987, encoding a protein of 613 amino acids with a deduced molecular mass of 67.708 kDa. The enzyme was shown to belong to the multicopper oxidase family. The 24131-laccase protein was confirmed to have oxidation activity against 2,6-dimethoxyphenol by ectopic expression in Escherichia coli. Laccase activity was significantly enhanced by feeding land crabs with plant diets. These data suggest that the enzyme plays an important role in the digestion of lignin in the guts of land crabs.

Characterisation of the enzyme transport path between shipworms and their bacterial symbionts

Background

Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), synthesised by endosymbionts living in specialised shipworm cells called bacteriocytes and located in the animal’s gills, play an important role in wood digestion in shipworms. However, the main site of lignocellulose digestion within these wood-boring molluscs, which contains both endogenous lignocellulolytic enzymes and prokaryotic enzymes, is the caecum, and the mechanism by which bacterial enzymes reach the distant caecum lumen has remained so far mysterious. Here, we provide a characterisation of the path through which bacterial CAZymes produced in the gills of the shipworm Lyrodus pedicellatus reach the distant caecum to contribute to the digestion of wood.

Results

Through a combination of transcriptomics, proteomics, X-ray microtomography, electron microscopy studies and in vitro biochemical characterisation, we show that wood-digesting enzymes produced by symbiotic bacteria are localised not only in the gills, but also in the lumen of the food groove, a stream of mucus secreted by gill cells that carries food particles trapped by filter feeding to the mouth. Bacterial CAZymes are also present in the crystalline style and in the caecum of their shipworm host, suggesting a unique pathway by which enzymes involved in a symbiotic interaction are transported to their site of action. Finally, we characterise in vitro four new bacterial glycosyl hydrolases and a lytic polysaccharide monooxygenase identified in our transcriptomic and proteomic analyses as some of the major bacterial enzymes involved in this unusual biological system.

Conclusion

Based on our data, we propose that bacteria and their enzymes are transported from the gills along the food groove to the shipworm’s mouth and digestive tract, where they aid in wood digestion.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01162-6.

New record of the wood-associated sea star Caymanostella, with notes on the phylogenetic position of the family Caymanostellidae (Asteroidea)

In 2016, three specimens of Caymanostella were collected from the Kuril-Kamchatka Trench area at depths of 5101–5134 m. Comparative morphological analysis revealed that the new specimens are similar to Caymanostella spinimarginata, the most geographically distant species (Atlantic Ocean). The new specimens were identified as C. cf. spinimarginata. Multilocus genetic data were obtained for the family Caymanostellidae for the first time in this study. Molecular evidence based on the analyses of three mitochondrial and two nuclear markers recovers the family Caymanostellidae as a sister-taxon to Ophidiasteridae (order Valvatida). Phylogenetic data indicate that morphological features, which were previously used to imply asterinid, xyloplacid or korethrasterid affinities for the family Caymanostellidae, emerged independently. It is suggested that the family Caymanostellidae should be placed within the order Valvatida.

Autochthonous production contributes to the diet of wood-boring invertebrates in temperate shallow water

Marine wood-boring invertebrates rapidly fragment coarse woody debris in the sea. These wood borers have the ability to digest wood cellulose, but other potential food sources have been less investigated. To assess the contribution of each potential food source to the diet of wood borers, we traced seasonal and environmental changes in δ¹³C of shipworms cultured under the same experimental conditions and related these changes to variations in δ¹³C of potential food sources, i.e., wood log and particulate organic matter (POM) by using multiple linear regression models rather than the Bayesian mixing model. Based on the standardized partial regression coefficients in the model, it became clear that wood-derived organic carbon was the main carbon source for the teredinids, and POM also accounted for 37.9% of the teredinids' carbon source. Furthermore, we clarified variations in supplemental nitrogen sources for the teredinids: one species depended on both POM and wood log, whereas the other three species depended on either POM or wood log for their nitrogen source. δ¹³C values of another wood-boring bivalve of Martesia (Pholadidae) increase as it grows, which suggests that the bivalve switches its feeding strategy from xylophagous to filter feeding as it grows. Wood borers are known to accelerate the transfer of organic materials derived from wood logs to marine ecosystems. However, this study suggests that autochthonous production strongly contribute to the diet of marine wood borers, helping them to decompose wood logs in temperate shallow water.

To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization

The transition to terrestrial environments by formerly aquatic species has occurred repeatedly in many animal phyla and lead to the vast diversity of extant terrestrial species. The differences between aquatic and terrestrial habitats are enormous and involved remarkable morphological and physiological changes. Convergent evolution of various traits is evident among phylogenetically distant taxa, but almost no information is available about the role of symbiotic microbiota in such transition. Here, we suggest that intertidal and terrestrial brachyuran crabs are a perfect model to study the evolutionary pathways and the ecological role of animal-microbiome symbioses, since their transition to land is happening right now, through a number of independent lineages. The microorganisms colonizing the gut of intertidal and terrestrial crabs are expected to play a major role to conquer the land, by reducing water losses and permitting the utilization of novel food sources. Indeed, it has been shown that the microbiomes hosted in the digestive system of terrestrial isopods has been critical to digest plant items, but nothing is known about the microbiomes present in the gut of truly terrestrial crabs. Other important physiological regulations that could be facilitated by microbiomes are nitrogen excretion and osmoregulation in the new environment. We also advocate for advances in comparative and functional genomics to uncover physiological aspects of these ongoing evolutionary processes. We think that the multidisciplinary study of microorganisms associated with terrestrial crabs will shed a completely new light on the biological and physiological processes involved in the sea-land transition.

Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks

More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems-salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose-an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.

Isopod holobionts as promising models for lignocellulose degradation

BACKGROUND

Isopods have colonized all environments, partly thanks to their ability to decompose the organic matter. Their enzymatic repertoire, as well as the one of their associated microbiota, has contributed to their colonization success. Together, these holobionts have evolved several interesting life history traits to degrade the plant cell walls, mainly composed of lignocellulose. It has been shown that terrestrial isopods achieve lignocellulose degradation thanks to numerous and diverse CAZymes provided by both the host and its microbiota. Nevertheless, the strategies for lignocellulose degradation seem more diversified in isopods, in particular in aquatic species which are the least studied. Isopods could be an interesting source of valuable enzymes for biotechnological industries of biomass conversion.

RESULTS

To provide new features on the lignocellulose degradation in isopod holobionts, shotgun sequencing of 36 metagenomes of digestive and non-digestive tissues was performed from several populations of four aquatic and terrestrial isopod species. Combined to the 15 metagenomes of an additional species from our previous study, as well as the host transcriptomes, this large dataset allowed us to identify the CAZymes in both the host and the associated microbial communities. Analyses revealed the dominance of Bacteroidetes and Proteobacteria in the five species, covering 36% and 56% of the total bacterial community, respectively. The identification of CAZymes and new enzymatic systems for lignocellulose degradation, such as PULs, cellulosomes and LPMOs, highlights the richness of the strategies used by the isopods and their associated microbiota.

CONCLUSIONS

Altogether, our results show that the isopod holobionts are promising models to study lignocellulose degradation. These models can provide new enzymes and relevant lignocellulose-degrading bacteria strains for the biotechnological industries of biomass conversion.

Review: The structure and function of cellulase (endo-β-1,4-glucanase) and hemicellulase (β-1,3-glucanase and endo-β-1,4-mannase) enzymes in invertebrates that consume materials ranging from microbes, algae to leaf litter

This review discusses the reaction catalysed, and the structure and function of the cellulase, endo-β-1,4-glucanase and the hemicellulase enzymes, β-1,3-glucanase and endo-β-1,4-mannase that are present in numerous invertebrate groups with a diverse range of feeding specialisations. These range from microbial deposit and filter feeders, micro and macrophagous algal feeders, omnivores to herbivorous leaf litter and wood feeders. Endo-β-1,4-glucanase from glycosyl hydrolase family 9 (GH9) digests cellulose like β-1,4-glucans from a range of materials. As it hydrolyses crystalline cellulose very slowly, it is a poor cellulase. Where tested, the enzyme has dual endo-β-1,4-glucanase and lichenase activity. Its presence does not necessarily indicate the ability of an animal to digest cellulose. It only indicates the ability to digest β-1,4-glucans and its function, which is discussed in this review, should be considered with reference to the substrates present in the diet. β-1,3-glucanase (laminarinase) belongs to glycosyl hydrolase family 16 (GH16) and hydrolyses β-1.3-glucans. These polysaccharides are present in the cell walls of algae, protozoans and yeast, and they also occur as storage polysaccharides within protozoans and algae. Depending on their site of expression, these enzymes may function as a digestive enzyme or may be involved in innate immunity. Enzymes present in the digestive fluids or tissues, would be digestive. Haemolymph GH16 proteins may be involved in innate immunity through the activation of the phenol oxidase system. Insect GH16 proteins expressed within the haemolymph have lost their catalytic residues and function as β-glucan binding proteins. In contrast, crustacean GH16 proteins expressed within the same tissue, have retained the catalytic residues and thus possibly their β-1,3-glucanase activity. The potential function of which is discussed. Endo-β-1,4-mannase from glycosyl hydrolase family 5, subfamily 10 (GH5_10) hydrolyses mannan, glucomannan and galactomannan. These hemicelluloses are present in the cell walls of plants and algae and also function as storage polysaccharides within legume and palm seeds. They are digestive enzymes whose high expression in some species suggests they are a major contributor to hemicellulose digestion. They may also provide the animal with substantial amounts of monosaccharides for energy.

Biofilm Improves Isopod Growth Independent of the Dietary Cellulose Content

Cellulose is an abundant source of carbon, accounting for more than 50% of foliage and 90% of woody tissues of plants. Despite the diversity of species that include living or dead plant tissue in their diets, the ability to digest cellulose through self-produced enzymatic machinery is considered rare in the animal kingdom. The majority of animals studied to date rely on the cellulolytic activity of symbiotic microorganisms in their digestive tract, with some evidence for a complementary action of endogenous cellulases. Terrestrial isopods have evolved a lifestyle including feeding on a lignocellulose diet. Whether isopods utilize both external and internal cellulases for digestion of a diet is still not understood. We experimentally manipulated the content of cellulose (30%, 60%, or 90%) and the amount of biofilm (small or large) in the offered food source and quantified growth and cellulolytic activity in the gut of the isopod Porcellio scaber. The presence of a visible biofilm significantly promoted isopod growth, regardless of the cellulose content in the diet. The activity of gut cellulases was not significantly affected by the amount of biofilm or the cellulose content. Our results do not support a significant contribution of either ingested or host enzymes to cellulose utilization in P. scaber. Cellulose might not represent a key nutrient for isopods and does not seem to affect the nutritional value of the diet-associated biofilm. We propose that it is the biofilm community that determines the quality of plant diet in terrestrial isopods and potentially also in other detrital plant feeders.

GeneHunt for rapid domain-specific annotation of glycoside hydrolases

The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.

Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

BACKGROUND

Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especially plant biomass, might be one of the reasons of their successful spread. All isopods, which feed on plants and their by-products, must be capable of lignocellulose degradation. This complex composite is the main component of plants and is therefore an important nutrient source for many living organisms. Its degradation requires a large repertoire of highly specialized Carbohydrate-Active enZymes (called CAZymes) which are produced by the organism itself and in some cases, by its associated microbiota. The acquisition of highly diversified CAZymes could have helped isopods to adapt to their diet and to their environment, especially during land colonization.

RESULTS

To test this hypothesis, isopod host CAZomes (i.e. the entire CAZyme repertoire) were characterized in marine, freshwater and terrestrial species through a transcriptomic approach. Many CAZymes were identified in 64 isopod transcriptomes, comprising 27 de novo datasets. Our results show that marine, freshwater and terrestrial isopods exhibit different CAZomes, illustrating different strategies for lignocellulose degradation. The analysis of variations of the size of CAZy families shows these are expanded in terrestrial isopods while they are contracted in aquatic isopods; this pattern is probably resulting from the evolution of the host CAZomes during the terrestrial adaptation of isopods. We show that CAZyme gene duplications and horizontal transfers can be involved in adaptive divergence between isopod CAZomes.

CONCLUSIONS

Our characterization of the CAZomes in 64 isopods species provides new insights into the evolutionary processes that enabled isopods to conquer various environments, especially terrestrial ones.

Not all animals need a microbiome

It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several ‘microbiome-free’ lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.

Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.

Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans

Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining.

Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod

Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the first-ever transcriptome assembly for this species, and found 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to differentially expressed genes, the most notable being "alkaloid metabolic process". Within this category, we found eight differentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.

Transcriptome-Guided Identification of Carbohydrate Active Enzymes (CAZy) from the Christmas Island Red Crab, Gecarcoidea natalis and a Vote for the Inclusion of Transcriptome-Derived Crustacean CAZys in Comparative Studies

The Christmas Island red crab, Gecarcoidea natalis, is an herbivorous land crab that consumes mostly fallen leaf litter. In order to subsist, G. natalis would need to have developed specialised digestive enzymes capable of supplying significant amounts of metabolisable sugars from this diet. To gain insights into the carbohydrate metabolism of G. natalis, a transcriptome assembly was performed, with a specific focus on identifying transcripts coding for carbohydrate active enzyme (CAZy) using in silico approaches. Transcriptome sequencing of the midgut gland identified 70 CAZy-coding transcripts with varying expression values. At least three newly discovered putative GH9 endo-β-1,4-glucanase ("classic cellulase") transcripts were highly expressed in the midgut gland in addition to the previously characterised GH9 and GH16 (β-1,3-glucanase) transcripts, and underscoring the utility of whole transcriptome in uncovering new CAZy-coding transcripts. A highly expressed transcript coding for GH5_10 previously missed by conventional screening of cellulase activity was inferred to be a novel endo-β-1,4-mannase in G. natalis with in silico support from homology modelling and amino acid alignment with other functionally validated GH5_10 proteins. Maximum likelihood tree reconstruction of the GH5_10 proteins demonstrates the phylogenetic affiliation of the G. natalis GH5_10 transcript to that of other decapods, supporting endogenous expression. Surprisingly, crustacean-derived GH5_10 transcripts were near absent in the current CAZy database and yet mining of the transcriptome shotgun assembly (TSA) recovered more than 100 crustacean GH5_10s in addition to several other biotechnological relevant CAZys, underscoring the unappreciated potential of the TSA database as a valuable resource for crustacean CAZys.

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

BACKGROUND

Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.

RESULTS

To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.

CONCLUSIONS

Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.

Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals

Background

Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated.

Results

We perform an exhaustive search for glycoside hydrolase (GH) genes from 21 genomes representing major bilaterian (Ecdysozoa, Spiralia, Echinodermata and Chordata) and basal metazoan (Porifera and Cnidaria) lineages. We also assessed the genome of a unicellular relative of Metazoa, Capsaspora owczarzaki and together with comparative analyses on 126 crustacean transcriptomes, we found that animals are living bioreactors at a microscale as they encode enzymatic suites for biomass decomposition. We identified a total of 16,723 GH homologs (2373 genes from animal genomes and 14,350 genes from crustacean transcriptomes) that are further classified into 60 GH families. Strikingly, through phylogenetic analyses, we observed that animal lignocellulosic enzymes have multiple origins, either inherited vertically over millions of years from a common ancestor or acquired more recently from non-animal organisms.

Conclusion

We have conducted a systematic and comprehensive survey of GH genes across major animal lineages. The ability of biomass decay appears to be determined by animals’ dietary strategies. Detritivores have genes that accomplish broad enzymatic functions while the number of GH families is reduced in animals that have evolved specialized diets. Animal GH candidates identified in this study will not only facilitate future functional genomics research but also provide an analysis platform to identify enzyme candidates with industrial potential.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4861-0) contains supplementary material, which is available to authorized users.

Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy

The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum

BACKGROUND

The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate.

RESULTS

The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. The catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs.

CONCLUSIONS

We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.

De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery

Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an average length of 641 bp were obtained and 19,915 unigenes were successfully annotated in four public databases. Only 9932 out of 19915 unigenes were commonly annotated by all four databases. In addition, 9609 unigenes were categorized into 54 function categories of Gene Ontology (GO), and 14,512 unigenes were successfully grouped into 25 functional categories of the EuKaryotic Orthologous Groups (KOG) database. Moreover, 11,507 unigenes were assigned to 228 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Out of 51,092 unigenes, a total of 4257 different microsatellites with motifs range from di- to hexa-nucleotide were identified from 3324 unigene sequences. Among 64 primer pairs selected for validation, 35 were successful in PCR amplification and 13 exhibited obvious repeat polymorphisms in the wild population of S. terebrans in Dongzhaigang (Hainan Island). The transcriptome dataset and the identified microsatellite markers (SSRs) will provide abundant information for researches on the discovery of new genes, metabolic mechanism and genetic diversity of S. terebrans.

Evolution and functional characterization of CAZymes belonging to subfamily 10 of glycoside hydrolase family 5 (GH5_10) in two species of phytophagous beetles

Hemicelluloses, such as xyloglucan, xylan and mannans, consist of a heterogeneous array of plant-derived polysaccharides that form the plant cell wall. These polysaccharides differ from each other in their structure and physiochemical properties, but they share a β-(1,4)-linked sugar backbone. Hemicelluloses can be hydrolyzed by plant-cell-wall-degrading enzymes (PCWDEs), which are widely distributed in phytopathogenic microbes. Recently, it has become apparent that phytophagous beetles also produce their own PCWDEs. Our previous work identified genes encoding putative mannanases belonging to the subfamily 10 of glycoside hydrolase (GH) family 5 (GH5_10) in the genomes of the leaf beetle, Gastrophysa viridula (Chrysomelidae, Chrysomelinae; one gene), and of the bean beetle, Callosobruchus maculatus (Chrysomelidae, Bruchinae; four genes). In contrast to proteins from other GH5 subfamilies, GH5_10 proteins are patchily distributed within the tree of life and have so far hardly been investigated. We addressed the following questions: Are beetle-derived GH5_10s active PCWDEs? How did they evolve? What is their physiological function? Using heterologous protein expression and enzymatic assays, we show that the G. viridula GH5_10 protein is an endo-β-1,4-mannanase. We also demonstrate that only one out of four C. maculatus GH5_10 proteins is an endo-β-1,4-mannanase, which has additional activity on carboxymethyl cellulose. Unexpectedly, another C. maculatus GH5_10 protein has evolved to use xylan instead of mannans as a substrate. RNAi experiments in G. viridula indicate (i) that the sole GH5_10 protein is responsible for breaking down mannans in the gut and (ii) that this breakdown may rather be accessory and may facilitate access to plant cell content, which is rich in nitrogen and simple sugars. Phylogenetic analyses indicate that coleopteran-derived GH5_10 proteins cluster together with Chelicerata-derived ones. Interestingly, other insect-derived GH5_10 proteins cluster elsewhere, suggesting insects have several independent evolutionary origins.

Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species

BACKGROUND

Growing global demands for crustacean food crop species have driven large investments in aquaculture research worldwide. However, large-scale production is susceptible to pathogen-mediated destruction particularly in developing economies. Thus, a thorough understanding of the immune system components of food crop species is imperative for research to combat pathogens.

RESULTS

Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of the class Malacostraca, which includes all food crop species. We identify 7407 malacostracan genes from 39 gene families implicated in different aspects of host defence and demonstrate dynamic evolution of innate immunity components within this group. Malacostracans have achieved flexibility in recognising infectious agents through divergent evolution and expansion of pathogen recognition receptors genes. Antiviral RNAi, Toll and JAK-STAT signal transduction pathways have remained conserved within Malacostraca, although the Imd pathway appears to lack several key components. Immune effectors such as the antimicrobial peptides (AMPs) have unique evolutionary profiles, with many malacostracan AMPs not found in other arthropods. Lastly, we describe four putative novel immune gene families, potentially representing important evolutionary novelties of the malacostracan immune system.

CONCLUSION

Our analyses across the broader Malacostraca have allowed us to not only draw analogies with other arthropods but also to identify evolutionary novelties in immune modulation components and form strong hypotheses as to when key pathways have evolved or diverged. This will serve as a key resource for future immunology research in crustacean food crops.

Efficient Cleavage of Lignin-Carbohydrate Complexes and Ultrafast Extraction of Lignin Oligomers from Wood Biomass by Microwave-Assisted Treatment with Deep Eutectic Solvent

Lignocellulosic biomass is an abundant and renewable resource for the production of biobased value-added fuels, chemicals, and materials, but its effective exploitation by an energy-efficient and environmentally friendly strategy remains a challenge. Herein, a facile approach for efficiently cleaving lignin-carbohydrate complexes and ultrafast fractionation of components from wood by microwave-assisted treatment with deep eutectic solvent is reported. The solvent was composed of sustainable choline chloride and oxalic acid dihydrate, and showed a hydrogen-bond acidity of 1.31. Efficient fractionation of lignocellulose with the solvent was realized by heating at 80 °C under 800 W microwave irradiation for 3 min. The extracted lignin showed a low molecular weight of 913, a low polydispersity of 1.25, and consisted of lignin oligomers with high purity (ca. 96 %), and thus shows potential in downstream production of aromatic chemicals. The other dissolved matter mainly comprised glucose, xylose, and hydroxymethylfurfural. The undissolved material was cellulose with crystal I structure and a crystallinity of approximately 75 %, which can be used for fabricating nanocellulose. Therefore, this work promotes an ultrafast lignin-first biorefinery approach while simultaneously keeping the undissolved cellulose available for further utilization. This work is expected to contribute to improving the economics of overall biorefining of lignocellulosic biomass.

'Venus trapped, Mars transits': Cu and Fe redox chemistry, cellular topography and in situ ligand binding in terrestrial isopod hepatopancreas

Woodlice efficiently sequester copper (Cu) in ‘cuprosomes' within hepatopancreatic ‘S' cells. Binuclear ‘B’ cells in the hepatopancreas form iron (Fe) deposits; these cells apparently undergo an apocrine secretory diurnal cycle linked to nocturnal feeding. Synchrotron-based µ-focus X-ray spectroscopy undertaken on thin sections was used to characterize the ligands binding Cu and Fe in S and B cells of Oniscus asellus (Isopoda). Main findings were: (i) morphometry confirmed a diurnal B-cell apocrine cycle; (ii) X-ray fluorescence (XRF) mapping indicated that Cu was co-distributed with sulfur (mainly in S cells), and Fe was co-distributed with phosphate (mainly in B cells); (iii) XRF mapping revealed an intimate morphological relationship between the basal regions of adjacent S and B cells; (iv) molecular modelling and Fourier transform analyses indicated that Cu in the reduced Cu⁺ state is mainly coordinated to thiol-rich ligands (Cu–S bond length 2.3 Å) in both cell types, while Fe in the oxidized Fe³⁺ state is predominantly oxygen coordinated (estimated Fe–O bond length of approx. 2 Å), with an outer shell of Fe scatterers at approximately 3.05 Å; and (v) no significant differences occur in Cu or Fe speciation at key nodes in the apocrine cycle. Findings imply that S and B cells form integrated unit-pairs; a functional role for secretions from these cellular units in the digestion of recalcitrant dietary components is hypothesized.

Macroinvertebrate community assembly on deep-sea wood falls in Monterey Bay is strongly influenced by wood type

Environmental filtering, including the influence of environmental constraints and biological interactions on species' survival, is known to significantly affect patterns of community assembly in terrestrial ecosystems. However, its role in regulating patterns and processes of community assembly in deep-sea environments is poorly studied. Here we investigated the role of wood characteristics in the assembly of deep-sea wood fall communities. Ten different wood species (substrata) that varied in structural complexity were sunk to a depth of 3,100 m near Monterey Bay, CA. In total, 28 wood parcels were deployed on the deep-sea bed. After 2 yr, the wood parcels were recovered with over 7,000 attached or colonizing macroinvertebrates. All macroinvertebrates were identified to the lowest taxonomic level possible, and included several undescribed species. Diversity indices and multivariate analyses of variance detected significant variation in the colonizing community assemblages among different wood substrata. Structural complexity seemed to be the primary factor altering community composition between wood substrata. For example, wood-boring clams were most abundant on solid logs, while small arthropods and limpets were more abundant on bundles of branches that provided more surface area and small, protected spaces to occupy. Other factors such as chemical defenses, the presence of bark, and wood hardness likely also played a role. Our finding that characteristics of woody debris entering the marine realm can have significant effects on community assembly supports the notion of ecological and perhaps evolutionarily significant links between land and sea.

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.

DOI:http://dx.doi.org/10.7554/eLife.20062.001

The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory.

Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available.

Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases.

Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production.

DOI:http://dx.doi.org/10.7554/eLife.20062.002

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface

BACKGROUND

Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.

RESULTS

The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.

CONCLUSIONS

Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.

The Terrestrial Isopod Microbiome: An All-in-One Toolbox for Animal-Microbe Interactions of Ecological Relevance

Bacterial symbionts represent essential drivers of arthropod ecology and evolution, influencing host traits such as nutrition, reproduction, immunity, and speciation. However, the majority of work on arthropod microbiota has been conducted in insects and more studies in non-model species across different ecological niches will be needed to complete our understanding of host–microbiota interactions. In this review, we present terrestrial isopod crustaceans as an emerging model organism to investigate symbiotic associations with potential relevance to ecosystem functioning. Terrestrial isopods comprise a group of crustaceans that have evolved a terrestrial lifestyle and represent keystone species in terrestrial ecosystems, contributing to the decomposition of organic matter and regulating the microbial food web. Since their nutrition is based on plant detritus, it has long been suspected that bacterial symbionts located in the digestive tissues might play an important role in host nutrition via the provisioning of digestive enzymes, thereby enabling the utilization of recalcitrant food compounds (e.g., cellulose or lignins). If this were the case, then (i) the acquisition of these bacteria might have been an important evolutionary prerequisite for the colonization of land by isopods, and (ii) these bacterial symbionts would directly mediate the role of their hosts in ecosystem functioning. Several bacterial symbionts have indeed been discovered in the midgut caeca of terrestrial isopods and some of them might be specific to this group of animals (i.e., Candidatus Hepatoplasma crinochetorum, Candidatus Hepatincola porcellionum, and Rhabdochlamydia porcellionis), while others are well-known intracellular pathogens (Rickettsiella spp.) or reproductive parasites (Wolbachia sp.). Moreover, a recent investigation of the microbiota in Armadillidium vulgare has revealed that this species harbors a highly diverse bacterial community which varies between host populations, suggesting an important share of environmental microbes in the host-associated microbiota. In this review, we synthesize our current knowledge on the terrestrial isopod microbiome and identify future directions to (i) fully understand the functional roles of particular bacteria (both intracellular or intestinal symbionts and environmental gut passengers), and (ii) whether and how the host-associated microbiota could influence the performance of terrestrial isopods as keystone species in soil ecosystems.

Exploring the bacterial gut microbiota of supralittoral talitrid amphipods

Talitrid amphipods (sandhoppers and beach fleas) are typical of the supralittoral zone. They are known to thrive on stranded materials, including detrital marine angiosperms and macroalgae, as well as occasional dead animals. In this work, the gut microbiota of five species of talitrid amphipods (Talitrus saltator, Talorchestia ugolinii, Sardorchestia pelecaniformis, Orchestia montagui and Orchestia stephenseni) collected in Sardinia (Italy) has been investigated through: i) metabarcoding analysis of the amplified 16S rRNA V4 region; and ii) quantification of family 48 glycosyl hydrolase genes (GHF48), involved in cellulose degradation. Results indicate that, though talitrid gut biodiversity is not directly related to taxon or sampling locality, the animals' digestive tracts may host species-specific bacterial communities. In particular, gut microbiota of O. montagui, an inhabitant of Posidonia banquettes and macro-algae mat, showed the greatest differences in taxonomic composition and the highest proportion of GHF48 genes with respect to 16S rRNA genes. These results suggest that the different talitrid species may host species-specific bacterial communities whose function could partially reflect the different microhabitats and food preferences of their host.

Combined Detoxification and In-situ Product Removal by a Single Resin During Lignocellulosic Butanol Production

Phragmites australis (an invasive plant in North America) was used as feedstock for ABE (acetone-butanol-ethanol) fermentation by Clostridium saccharobutylicum. Sulphuric acid pretreated phragmites hydrolysate (SAEH) without detoxification inhibited butanol production (0.73 g/L butanol from 30 g/L sugars). The treatment of SAEH with resin L-493 prior the fermentation resulted in no inhibitory effects and an ABE titer of 14.44 g/L, including 5.49 g/L butanol was obtained, corresponding to an ABE yield and productivity of 0.49 g/g and 0.60 g/L/h, respectively. Dual functionality of the resin was realized by also using it as an in-situ product removal agent. Integrating in-situ product removal allowed for the use of high substrate concentrations without the typical product inhibition. Resin-detoxified SAEH was supplemented with neat glucose and an effective ABE titer of 33 g/L (including 13.7 g/L acetone, 16.4 g/L butanol and 1.9 g/L ethanol) was achieved with resin-based in-situ product removal, corresponding to an ABE yield and productivity of 0.41 g/g and 0.69 g/L/h, respectively. Both detoxification of the substrate and the products was achieved by the same resin, which was added prior the fermentation. Integrating hydrolysate detoxification and in-situ butanol removal in a batch process through single resin can potentially simplify cellulosic butanol production.

Biochemical and Structural Characterizations of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Level of Conservation between Distant Phylogenetic Trees of Life

Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) are enzymes commonly employed in plant cell wall degradation across eukaryotic kingdoms of life, as they provide significant hydrolytic potential in cellulose turnover. To date, many fungal GH7 CBHs have been examined, yet many questions regarding structure-activity relationships in these important natural and commercial enzymes remain. Here, we present the crystal structures and a biochemical analysis of two GH7 CBHs from social amoeba: Dictyostelium discoideum Cel7A (DdiCel7A) and Dictyostelium purpureum Cel7A (DpuCel7A). DdiCel7A and DpuCel7A natively consist of a catalytic domain and do not exhibit a carbohydrate-binding module (CBM). The structures of DdiCel7A and DpuCel7A, resolved to 2.1 Å and 2.7 Å, respectively, are homologous to those of other GH7 CBHs with an enclosed active-site tunnel. Two primary differences between the Dictyostelium CBHs and the archetypal model GH7 CBH, Trichoderma reesei Cel7A (TreCel7A), occur near the hydrolytic active site and the product-binding sites. To compare the activities of these enzymes with the activity of TreCel7A, the family 1 TreCel7A CBM and linker were added to the C terminus of each of the Dictyostelium enzymes, creating DdiCel7ACBM and DpuCel7ACBM, which were recombinantly expressed in T. reesei DdiCel7ACBM and DpuCel7ACBM hydrolyzed Avicel, pretreated corn stover, and phosphoric acid-swollen cellulose as efficiently as TreCel7A when hydrolysis was compared at their temperature optima. The Ki of cellobiose was significantly higher for DdiCel7ACBM and DpuCel7ACBM than for TreCel7A: 205, 130, and 29 μM, respectively. Taken together, the present study highlights the remarkable degree of conservation of the activity of these key natural and industrial enzymes across quite distant phylogenetic trees of life.

IMPORTANCE

GH7 CBHs are among the most important cellulolytic enzymes both in nature and for emerging industrial applications for cellulose breakdown. Understanding the diversity of these key industrial enzymes is critical to engineering them for higher levels of activity and greater stability. The present work demonstrates that two GH7 CBHs from social amoeba are surprisingly quite similar in structure and activity to the canonical GH7 CBH from the model biomass-degrading fungus T. reesei when tested under equivalent conditions (with added CBM-linker domains) on an industrially relevant substrate.

Lignocellulose degradation mechanisms across the Tree of Life

Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.

Purification and characterization of a hemocyanin (Hemo1) with potential lignin-modification activities from the wood-feeding termite, Coptotermes formosanus Shiraki

Coptotermes formosanus Shiraki is a well-known wood-feeding termite, which can degrade not only cellulose and hemicellulose polysaccharides, but also some aromatic lignin polymers with its enzyme complex to the woody biomass. In this study, a very abundant protein was discovered and purified, using a three-step column chromatography procedure, from the tissue homogenate of the salivary glands and the gut of C. formosanus. Mass spectrometric analysis and the following peptide searching against the mRNA database toward this termite species indicated that the novel protein was a hemocyanin enzyme, termed as Hemo1, which further exhibited a strong oxidase activity in the substrate bioassays toward ABTS [2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)], as well as other aromatic analogues, such as catechol and veratryl alcohols. This oxidative protein was an acid-favored enzyme with a molecular weight at 82 kDa, and highly active at 80 °C. These findings indicated that the novel protein, hemocyanin, discovered from the gut system of C. formosanus, might be an important ligninolytic enzyme involved in the biomass pretreatment processing, which will potentially enhance the digestibility and utilization of biomass polysaccharides in termite digestive systems.

Biogeography of wood-boring crustaceans (Isopoda: Limnoriidae) established in European coastal waters

Marine wood-borers of the Limnoriidae cause great destruction to wooden structures exposed in the marine environment. In this study we collated occurrence data obtained from field surveys, spanning over a period of 10 years, and from an extensive literature review. We aimed to determine which wood-boring limnoriid species are established in European coastal waters; to map their past and recent distribution in Europe in order to infer species range extension or contraction; to determine species environmental requirements using climatic envelopes. Of the six species of wood-boring Limnoria previously reported occurring in Europe, only Limnoria lignorum, L. quadripunctata and L. tripunctata are established in European coastal waters. L. carinata and L. tuberculata have uncertain established status, whereas L. borealis is not established in European waters. The species with the widest distribution in Europe is Limnoria lignorum, which is also the most tolerant species to a range of salinities. L. quadripunctata and L. tripunctata appear to be stenohaline. However, the present study shows that both L. quadripunctata and L. tripunctata are more widespread in Europe than previous reports suggested. Both species have been found occurring in Europe since they were described, and their increased distribution is probably the results of a range expansion. On the other hand L. lignorum appears to be retreating poleward with ocean warming. In certain areas (e.g. southern England, and southern Portugal), limnoriids appear to be very abundant and their activity is rivalling that of teredinids. Therefore, it is important to monitor the distribution and destructive activity of these organisms in Europe.

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health.

Insect-derived enzymes: a treasure for industrial biotechnology and food biotechnology

Insects are the most diverse group of organisms on earth, colonizing almost every ecological niche of the planet. To survive in various and sometimes extreme habitats, insects have established diverse biological and chemical systems. Core components of these systems are enzymes that enable the insects to feed on diverse nutrient sources. The enzymes are produced by either the insects themselves (homologous) or by symbiotic organisms located in the insects' bodies or in their nests (heterologous). The use of these insect-associated enzymes for applications in the fields of food biotechnology and industrial (white) biotechnology is gaining more and more interest. Prominent examples of insect-derived enzymes include peptidases, amylases, lipases, and β-D-glucosidases. Highly potent peptidases for the degradation of gluten, a storage protein that can cause intestinal disorders, may be received from grain pests. Several insects, such as bark and ambrosia beetles and termites, are able to feed on wood. In the field of white biotechnology, their cellulolytic enzyme systems of mainly endo-1,4-β-D-glucanases and β-D-glucosidases can be employed for saccharification of the most prominent polymer on earth-cellulose.

Endogenous cellulase enzymes in the stick insect (Phasmatodea) gut

High cellulase (endo-beta-1,4-glucanase) activity was detected in the anterior midgut of the walking stick (Phasmatodea) Eurycantha calcarata. The enzyme was isolated and analyzed via mass spectrometry. RT-PCR revealed two endoglucanase genes, EcEG1 and EcEG2. Mascot analysis of the purified enzyme confirms it to be the product of gene EcEG1. Homologous cDNAs were also isolated from a distantly related species, Entoria okinawaensis, suggesting a general distribution of cellulase genes in phasmids. Phasmid cellulases showed high homology to endogenously-produced glycoside hydrolase family 9 (GH9) endoglucanases from insects, especially to those of termites, cockroaches, and crickets. The purified E. calcarata enzyme showed clear antigency against an anti-serum for termite GH9 cellulase, which, together with the sequence homology, further suggests an endogenous origin of the enzyme. This discovery suggests a possible nutritive value for cellulose in the leaf-feeding phasmids, unlike in herbivorous Lepidoptera.

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.