Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.

Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy

BACKGROUND

Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS

The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS

Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.

Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods

Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.

Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti

Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.

Evidence of cospeciation between termites and their gut bacteria on a geological time scale

Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.

New insights into the coevolutionary history of termites and their gut flagellates: Description of Retractinympha glossotermitis gen. nov. sp. nov. (Retractinymphidae fam. nov.)

Lower termites harbor diverse consortia of symbiotic gut flagellates. Despite numerous evidence for co-cladogenesis, the evolutionary history of these associations remains unclear. Here, we present Retractinymphidae fam. nov., a monogeneric lineage of Trichonymphida from Serritermitidae. Although Retractinympha glossotermitis gen. nov. sp. nov. morphologically resembles members of the genus Pseudotrichonympha, phylogenetic analysis identified it as sister group of the Teranymphidae. We compared morphology and ultrastructure of R. glossotermitis to that of Pseudotrichonympha and other Teranymphidae, including the so-far undescribed Pseudotrichonympha solitaria sp. nov. from Termitogeton planus (Rhinotermitidae). Like all Teranymphidae, R. glossotermitis is a large, elongated flagellate with a bilaterally symmetric rostrum, an anterior, flagella-free operculum, and an internal rostral tube. However, it is readily distinguished by the length of its rostral flagella, which never exceeds that of the postrostral flagella, and its retractable anterior end. Inclusion of the hitherto unstudied Stylotermes halumicus (Stylotermitidae) in our survey of trichonymphid flagellates in Neoisoptera confirmed that the combined presence of Heliconympha and Retractinympha and absence of Pseudotrichonympha is unique to Serritermitidae. The close phylogenetic relatedness of Heliconympha in Serritermitidae to the spirotrichosomid flagellates in Stolotermitidae provides strong support for their acquisition by horizontal transmission.

The functional evolution of termite gut microbiota

BACKGROUND

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota.

RESULTS

We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways.

CONCLUSIONS

Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.

A new family for 'termite gut treponemes': description of Breznakiellaceae fam. nov., Gracilinema caldarium gen. nov., comb. nov., Leadbettera azotonutricia gen. nov., comb. nov., Helmutkoenigia isoptericolens gen. nov., comb. nov., and Zuelzera stenostrepta gen. nov., comb. nov., and proposal of Rectinemataceae fam. nov

The intestinal tracts of termites are abundantly colonized by a diverse assemblage of spirochetes. Most of them belong to 'termite cluster I', a monophyletic group within the radiation of the genus Treponema that occurs exclusively in termite guts. Phylogenomic analysis revealed that members of the genus Treponema are extremely diverse and represent two separate, family-level lineages: the Treponemataceae sensu stricto, which comprise the majority of the validly described Treponema species, and a second lineage that comprises the remaining members of the genus Treponema, including all members of 'termite cluster I' from termites and the recently isolated Breznakiella homolactica from cockroaches. Here, we present the formal description of Breznakiellaceae fam. nov. and of the new genera required to accommodate the misplaced Treponema species in the new family as new combinations (Leadbettera azotonutricia, Gracilinema caldarium, Helmutkoenigia isoptericolens and Zuelzera stenostrepta). To avoid paraphyly of Treponemataceae, we propose Rectinemataceae fam. nov. to include the genus Rectinema.

The hydrogen threshold of obligately methyl-reducing methanogens

Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.

Characterization and phylogenomic analysis of Breznakiella homolactica gen. nov. sp. nov. indicate that termite gut treponemes evolved from non-acetogenic spirochetes in cockroaches

Spirochetes of the genus Treponema are surprisingly abundant in termite guts, where they play an important role in reductive acetogenesis. Although they occur in all termites investigated, their evolutionary origin is obscure. Here, we isolated the first representative of 'termite gut treponemes' from cockroaches, the closest relatives of termites. Phylogenomic analysis revealed that Breznakiella homolactica gen. nov. sp. nov. represents the most basal lineage of the highly diverse 'termite cluster I', a deep-branching sister group of Treponemataceae (fam. 'Termitinemataceae') that was present already in the cockroach ancestor of termites and subsequently coevolved with its host. Breznakiella homolactica is obligately anaerobic and catalyses the homolactic fermentation of both hexoses and pentoses. Resting cells produced acetate in the presence of oxygen. Genome analysis revealed the presence of pyruvate oxidase and catalase, and a cryptic potential for the formation of acetate, ethanol, formate, CO₂ and H₂ - the fermentation products of termite gut isolates. Genes encoding key enzymes of reductive acetogenesis, however, are absent, confirming the hypothesis that the ancestral metabolism of the cluster was fermentative, and that the capacity for acetogenesis from H₂ plus CO₂ - the most intriguing property among termite gut treponemes - was acquired by lateral gene transfer.

Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts - A Genome-Centric Analysis

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO₂ via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C₁ carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO₂ reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.

Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

"Higher" termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, for example, Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.

Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

BACKGROUND

Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter.

RESULTS

The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites.

CONCLUSION

Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

Rampant Host Switching Shaped the Termite Gut Microbiome

The gut microbiota of animals exert major effects on host biology [1]. Although horizontal transfer is generally considered the prevalent route for the acquisition of gut bacteria in mammals [2], some bacterial lineages have co-speciated with their hosts on timescales of several million years [3]. Termites harbor a complex gut microbiota, and their advanced social behavior provides the potential for long-term vertical symbiont transmission, and co-evolution of gut symbionts and host [4-6]. Despite clear evolutionary patterns in the gut microbiota of termites [7], a consensus on how microbial communities were assembled during termite diversification has yet to be reached. Although some studies have concluded that vertical transmission has played a major role [8, 9], others indicate that diet and gut microenvironment have been the primary determinants shaping microbial communities in termite guts [7, 10]. To address this issue, we examined the gut microbiota of 94 termite species, through 16S rRNA metabarcoding. We analyzed the phylogeny of 211 bacterial lineages obtained from termite guts, including their closest relatives from other environments, which were identified using BLAST. The results provided strong evidence for rampant horizontal transfer of gut bacteria between termite host lineages. Although the majority of termite-derived phylotypes formed large monophyletic groups, indicating high levels of niche specialization, numerous other clades were interspersed with bacterial lineages from the guts of other animals. Our results indicate that "mixed-mode" transmission, which combines colony-to-offspring vertical transmission with horizontal colony-to-colony transfer, has been the primary driving force shaping the gut microbiota of termites.

Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting?

Mutualistic associations of bacteria and invertebrates are widespread and encompass an enormous diversity on the side of both partners. The advantages gained from the symbiosis favour reciprocal adaptations that increase the stability of the association and can lead to codiversification of symbiont and host. While numerous examples of a strictly vertical transfer of the symbionts from parent to offspring among intracellular associations abound, little is known about the fidelity of the partners in extracellular associations, where symbionts colonize the surface or body cavity of their host. In this issue of Molecular Ecology, Zimmermann et al. () investigated the evolutionary history of the symbiotic association between a monophyletic clade of sulphur-oxidizing Gammaproteobacteria and two distantly related lineages of marine worms (nematodes and annelids). The study supports the surprising conclusion that partner fidelity does not necessarily increase with the intimacy of the association. Ectosymbionts on the cuticle of the nematodes seem to be cospeciating with their hosts, whereas endosymbionts housed in the body cavity of the annelids must have originated multiple times, probably by host switching, from ectosymbionts of sympatric nematodes. This excellent case study on the evolutionary history of invertebrate-microbe interactions supports the emerging concept that the co-evolutionary processes shaping such mutualistic symbioses include both codiversification and ecological fitting.

High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates

Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers. Here, we present a robust phylogenetic framework based on the near-full-length 16S-23S rRNA gene region of a diverse set of Endomicrobia from termites and cockroaches, which also allowed us to classify the shorter reads from previous studies. Our data revealed that endosymbionts arose independently at least four times from different free-living lineages, which were already present in ancestral cockroaches but became associated with their respective hosts long after the digestive symbiosis between termites and flagellates had been established. Pyrotag sequencing revealed that the proportion of putatively free-living lineages increased, when all flagellates and their symbionts were removed from the gut of lower termites by starvation, starch feeding or hyperbaric oxygen, but results varied between different methods.

The complete mitochondrial genomes of the higher termitesLabiotermes labralisandEmbiratermes neotenicus(Termitidae: Syntermitinae)

The complete mitochondrial genomes (mitogenomes) of two higher termites were reconstructed from the metagenomes of individual gut compartments with more than 2000-fold coverage. The circular mitogenomes of Labiotermes labralis (accession number KY436201) and Embiratermes neotenicus (accession number KY436202) have a length of 15,935 and 15,868 bp and an overall G + C content of 30.7 mol% and 33.7 mol%, respectively, and both have an asymmetric nucleotide composition. Genome structure and orientation are the same as in other termites and in the ancestral insect mitogenome. These data further expand arthropod mitogenome databases, which have become an important resource in ecological, phylogenetic and evolutionary studies.

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites

Symbiotic digestion of lignocellulose in higher termites (family Termitidae) is accomplished by an exclusively prokaryotic gut microbiota. By deep sequencing of amplified 16S rRNA genes, we had identified diet as the primary determinant of bacterial community structure in a broad selection of termites specialized on lignocellulose in different stages of humification. Here, we increased the resolution of our approach to account for the pronounced heterogeneity in microenvironmental conditions and microbial activities in the major hindgut compartments. The community structure of consecutive gut compartments in each species strongly differed, but that of homologous compartments clearly converged, even among unrelated termites. While the alkaline P1 compartments of all termites investigated contained specific lineages of Clostridiales, the posterior hindgut compartments (P3, P4) differed between feeding groups and were predominantly colonized by putatively fiber-associated lineages of Spirochaetes, Fibrobacteres and the TG3 phylum (wood and grass feeders) or diverse assemblages of Clostridiales and Bacteroidetes (humus and soil feeders). The results underscore that bacterial community structure in termite guts is driven by microenvironmental factors, such as pH, available substrates and gradients of O₂ and H₂, and inspire investigations on the functional roles of specific bacterial taxa in lignocellulose and humus digestion.

Genome analysis of 'Candidatus Ancillula trichonymphae', first representative of a deep-branching clade of Bifidobacteriales, strengthens evidence for convergent evolution in flagellate endosymbionts

The flagellate protists in the hindgut of lower termites play an essential role in the digestion of lignocellulose. Most flagellate species are associated with host-specific symbionts from various bacterial lineages, which typically lack cultured representatives. In this study, we analyzed the genome of 'Candidatus Ancillula trichonymphae', an endosymbiont of Trichonympha flagellates from dry-wood termites, which represents a novel, family-level lineage of uncultured Actinobacteria encountered so far only in termite guts. The draft genome of 'Ca. A. trichonymphae' (ca. 1.48 Mbp; 95% complete) revealed a purely fermentative metabolism that is probably fueled by xylose, N-acetyl-glucosamine and glycerol 3-phosphate acquired from the flagellate host. The absence of fructose bisphosphate aldolase and the presence of a complete gene set encoding the phosphoketolase pathway underscore the sister position of the new lineage to Bifidobacteriaceae. The preservation of the pathways for the assimilation of ammonia and the synthesis of 18 amino acids and several cofactors and vitamins suggests that 'Ca. A. trichonymphae' - like other endosymbionts of termite gut flagellates - provides essential amino acids and vitamins to its host. Our findings corroborate the emerging concept that numerous lineages of unrelated flagellate endosymbionts have convergently evolved to fill similar ecological niches.

Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae

Two novel, obligately anaerobic Firmicutes from the family Erysipelotrichaceae were isolated from the intestinal tracts of a cockroach (strain ErySL, Shelfordella lateralis) and a scarab beetle larva (strain Pei061, Pachnoda ephippiata). Phylogenetic analysis indicated that the strains belong to a monophyletic group of hitherto uncultured bacteria from insect guts that are only distantly related to any described species (<90% 16S rRNA gene sequence similarity). Ultrastructural analysis revealed a Gram-positive cell envelope and, in the case of strain ErySL, a wide electron-lucent space between the cytoplasmic membrane and cell wall. In older cultures, cells formed pleomorphic rods with a thicker peptidoglycan layer. Both strains were obligately anaerobic and fermented glucose to formate, ethanol, and acetate as major products, but strain Pei061 tolerated up to 1% oxygen in the headspace. The same type of metabolism was observed with Erysipelothrix inopinata, except that the latter grew, albeit poorly, even under air. However, previous claims of a microaerophilic or facultatively anaerobic metabolism in the genus Erysipelothrix could not be substantiated. Based on phenotypic and phylogenetic evidence, we propose to classify the isolates as members of a new genus, Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., with strain ErySL(T) (=DSM 28867(T)=JCM 30190(T)) and strain Pei061(T) (=DSM 16784(T)=JCM 30191(T)) as type strains, and provide an emended description of the family Erysipelotrichaceae.

Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model

The gut microbiota of termites and cockroaches represents complex metabolic networks of many diverse microbial populations. The distinct microenvironmental conditions within the gut and possible interactions among the microorganisms make it essential to investigate how far the metabolic properties of pure cultures reflect their activities in their natural environment. We established the cockroach Shelfordella lateralis as a gnotobiotic model and inoculated germfree nymphs with two bacterial strains isolated from the guts of conventional cockroaches. Fluorescence microscopy revealed that both strains specifically colonized the germfree hindgut. In diassociated cockroaches, the facultatively anaerobic strain EbSL (a new species of Enterobacteriaceae) always outnumbered the obligately anaerobic strain FuSL (a close relative of Fusobacterium varium), irrespective of the sequence of inoculation, which showed that precolonization by facultatively anaerobic bacteria does not necessarily favor colonization by obligate anaerobes. Comparison of the fermentation products of the cultures formed in vitro with those accumulated in situ indicated that the gut environment strongly affected the metabolic activities of both strains. The pure cultures formed the typical products of mixed-acid or butyrate fermentation, whereas the guts of gnotobiotic cockroaches accumulated mostly lactate and acetate. Similar shifts toward more-oxidized products were observed when the pure cultures were exposed to oxygen, which corroborated the strong effects of oxygen on the metabolic fluxes previously observed in termite guts. Oxygen microsensor profiles of the guts of germfree, gnotobiotic, and conventional cockroaches indicated that both gut tissue and microbiota contribute to oxygen consumption and suggest that the oxygen status influences the colonization success.

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

BACKGROUND

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown.

RESULTS

Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes.

CONCLUSION

Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont

Long-term vertical transmission of intracellular bacteria causes massive genomic erosion and results in extremely small genomes, particularly in ancient symbionts. Genome reduction is typically preceded by the accumulation of pseudogenes and proliferation of mobile genetic elements, which are responsible for chromosome rearrangements during the initial stage of endosymbiosis. We compared the genomes of an endosymbiont of termite gut flagellates, “Candidatus Endomicrobium trichonymphae,” and its free-living relative Endomicrobium proavitum and discovered many remnants of restriction-modification (R-M) systems that are consistently associated with genome rearrangements in the endosymbiont genome. The rearrangements include apparent insertions, transpositions, and the duplication of a genomic region; there was no evidence of transposon structures or other mobile elements. Our study reveals a so far unrecognized mechanism for genome rearrangements in intracellular symbionts and sheds new light on the general role of R-M systems in genome evolution.

Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus

Fungus-cultivating termites (Macrotermitinae) possess an elaborate strategy of lignocellulose digestion. It involves a lignocellulose-degrading fungal symbiont (genus Termitomyces), a diverse gut microbiota and a characteristic labour division in food processing. In this study, using pyrotag sequencing and electron microscopy, we analysed the bacterial microbiota in the hindgut of Odontotermes formosanus and its fungus comb to investigate the spatial organization, establishment and temporal succession of the bacterial communities colonizing specific microhabitats. Our results document strong differences between the communities at the hindgut epithelium and the luminal fluid of newly moulted, young and old worker termites. The differences in community structure were consistent with the density, morphology and spatial distribution of bacterial cells and the pools of microbial metabolites in the hindgut compartment, underlining that both gut development and the age-specific changes in diet affect the composition and functional role of their gut microbiota. These findings provide strong support for the concept that changes in diet and gut environment are important determinants of community structure because they create new niches for microbial symbionts.

Diet is the primary determinant of bacterial community structure in the guts of higher termites

The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.

Endomicrobium proavitum, the first isolate of Endomicrobia class. nov. (phylum Elusimicrobia)--an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase

The bacterial tree contains many deep-rooting clades without any cultured representatives. One such clade is 'Endomicrobia', a class-level lineage in the phylum Elusimicrobia represented so far only by intracellular symbionts of termite gut flagellates. Here, we report the isolation and characterization of the first free-living member of this clade from sterile-filtered gut homogenate of defaunated (starch-fed) Reticulitermes santonensis. Strain Rsa215 is a strictly anaerobic ultramicrobacterium that grows exclusively on glucose, which is fermented to lactate, acetate, hydrogen and CO2. Ultrastructural analysis revealed a Gram-negative cell envelope and a peculiar cell cycle. The genome contains a single set of nif genes that encode homologues of Group IV nitrogenases, which were so far considered to have functions other than nitrogen fixation. We documented nitrogenase activity and diazotrophic growth by measuring acetylene reduction activity and (15)N2 incorporation into cell mass, and demonstrated that transcription of nifH and nitrogenase activity occur only in the absence of ammonium. Based on the ancestral relationship to 'Candidatus Endomicrobium trichonymphae' and other obligate endosymbionts, we propose the name 'Endomicrobium proavitum' gen. nov., sp. nov. for the first isolate of this lineage and the name 'Endomicrobia' class. nov. for the entire clade.

Population structure of Endomicrobia in single host cells of termite gut flagellates (Trichonympha spp.)

The gut microbiota of many phylogenetically lower termites is dominated by the cellulolytic flagellates of the genus Trichonympha, which are consistently associated with bacterial symbionts. In the case of Endomicrobia, an unusual lineage of endosymbionts of the Elusimicrobia phylum that is also present in other gut flagellates, previous studies have documented strict host specificity, leading to the cospeciation of "Candidatus Endomicrobium trichonymphae" with their respective flagellate hosts. However, it currently remains unclear whether one Trichonympha species is capable of harboring more than one Endomicrobia phylotype. In the present study, we selected single Trichonympha cells from the guts of Zootermopsis nevadensis and Reticulitermes santonensis and characterized their Endomicrobia populations based on internal transcribed spacer (ITS) region sequences. We found that each host cell harbored a homogeneous population of symbionts that were specific to their respective host species, but phylogenetically distinct between each host lineage, corroborating cospeciation being caused by vertical inheritance. The experimental design of the present study also allowed for the identification of an unexpectedly large amount of tag-switching between samples, which indicated that any high-resolution analysis of microbial community structures using the pyrosequencing technique has to be interpreted with great caution.

New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”

The recently discovered seventh order of methanogens, the Methanomassiliicoccales (previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “Candidatus Methanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO2 reduction to methyl coenzyme Mand produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that Methanomassiliicoccales employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic Methanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F420:methanophenazine oxidoreductase (Fpo) of Methanosarcinales butlacks an F420-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in Methanosaeta thermophila. Since all Methanomassiliicoccales also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), wepropose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin: heterodisulfideoxidoreductase. The dual function of heterodisulfide in Methanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.

Physicochemical conditions, metabolites and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae)

While the gut microbiota of termites and its role in symbiotic digestion have been studied for decades, little is known about the bacteria colonizing the intestinal tract of the distantly related wood-feeding cockroaches (Blaberidae: Panesthiinae). Here, we show that physicochemical gut conditions and microbial fermentation products in the gut of Panesthia angustipennis resemble that of other cockroaches. Microsensor measurements confirmed that all gut compartments were anoxic at the center and had a slightly acidic to neutral pH and a negative redox potential. While acetate dominated in all compartments, lactate and hydrogen accumulated only in the crop. The high, hydrogen-limited rates of methane emission from living cockroaches were in agreement with the restriction of F420-fluorescent methanogens to the hindgut. The gut microbiota of both P. angustipennis and Salganea esakii differed strongly between compartments, with the highest density and diversity in the hindgut, but similarities between homologous compartments of both cockroaches indicated a specificity of the microbiota for their respective habitats. While some lineages were most closely related to the gut microbiota of omnivorous cockroaches and wood- or litter-feeding termites, others have been encountered also in vertebrates, reinforcing the hypothesis that strong environmental selection drives community structure in the cockroach gut.

The complete mitogenomes of six higher termite species reconstructed from metagenomic datasets (Cornitermes sp., Cubitermes ugandensis, Microcerotermes parvus, Nasutitermes corniger, Neocapritermes taracua, and Termes hospes)

We reconstructed the complete mitochondrial genomes of six higher termite species from metagenomic datasets of their isolated hindgut compartments. The sequencing reads were retrieved and assembled with the mitochondrial-baiting and iterative-mapping algorithm (MITObim), which yielded closed mitogenomes without additional finishing efforts (average coverage ranging from 2300- to 17,000-fold). The genomes ranged from 16.1 to 17.6 kbp in size and had G+C contents between 32 and 35 mol%; each contained the same 37 genes present also in the mitochondria of other termite species. Our study substantially increases the number of termite mitogenomes available for phylogenetic studies and offers a facile strategy for identifying host species in metagenomic studies of their associated microbiota.

Microprofiles of oxygen, redox potential, and pH, and microbial fermentation products in the highly alkaline gut of the saprophagous larva of Penthetria holosericea (Diptera: Bibionidae)

The saprophagous larvae of bibionid flies harbor bacteria in their alkaline intestinal tracts, but little is known about the contribution of the gut microbiota to the digestion of their recalcitrant diet. In this study, we measured oxygen and hydrogen partial pressure, redox potential and pH in the midgut, gastric caeca and hindgut of larvae of the bibionid fly Penthetria holosericea with Clark-type O2 and H2 microsensors, platinum redox microelectrodes, and LIX-type pH microelectrodes. The center of the midgut lumen was anoxic, whereas gastric caeca and hindgut were hypoxic. However, redox potential profiles indicated oxidizing conditions throughout the gut, with lowest values in the midgut (+20 to +60mV). Hydrogen production was not detected. The midgut was extremely alkaline (pH around 11), whereas hindgut and gastric caeca were neutral to slightly alkaline. While HPLC analysis showed high concentrations of glucose in the midgut (15mM) and gastric caeca (27mM), the concentrations of microbial fermentation products such as lactate (2-4mM), acetate (<1mM) and succinate (<0.5mM) were low in all gut regions, suggesting that the contribution of microorganisms to the digestive process, particularly in the alkaline midgut, is only of minor importance. We conclude that the digestive strategy of the saprophytic larva of P. holosericea, which feeds selectively on decomposed leaves and its own microbe-rich faeces, differs fundamentally from those of detritivorous and humivorous insects, which host a highly active, fermentative microbiota in their alkaline midgut or hindgut compartments.

Pyrotag sequencing of the gut microbiota of the cockroach Shelfordella lateralis reveals a highly dynamic core but only limited effects of diet on community structure

Although blattid cockroaches and termites share a common ancestor, their diets are distinctly different. While termites consume a highly specialized diet of lignocellulose, cockroaches are omnivorous and opportunistic feeders. The role of the termite gut microbiota has been studied intensively, but little is known about the cockroach gut microbiota and its function in digestion and nutrition, particularly the adaptation to different diets. Our analyses of the bacterial gut microbiota of the blattid cockroach Shelfordella lateralis combining terminal restriction fragment length polymorphism of their 16S rRNA genes with physiological parameters (microbial metabolites, hydrogen and methane emission) indicated substantial variation between individuals but failed to identify any diet-related response. Subsequent deep-sequencing of the 16S rRNA genes of the colonic gut microbiota of S. lateralis fed either a high- or a low-fiber diet confirmed the absence of bacterial taxa that responded to diet. Instead, we found a small number of abundant phylotypes that were consistently present in all samples and made up half of the community in both diet groups. They varied strongly in abundance between individual samples at the genus but not at the family level. The remaining phylotypes were inconsistently present among replicate batches. Our findings suggest that S. lateralis harbors a highly dynamic core gut microbiota that is maintained even after fundamental dietary shifts, and that any dietary effects on the gut community are likely to be masked by strong individual variations.