De novo metatranscriptomic exploration of gene function in the millipede holobiont

Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.

Metatranscriptomic holobiont analysis of carbohydrate-active enzymes in the millipede Telodeinopus aoutii (Diplopoda, Spirostreptida)

As important decomposers of soil organic matter, millipedes contribute to lignocellulose decomposition and nutrient cycling. The degradation of lignocellulose requires the action of several carbohydrate-active enzymes (CAZymes) and, in most invertebrates, depends on the activity of mutualistic gut microorganisms. To address the question of the importance of the microbiota and endogenous (host) enzymes in digestive processes in millipedes, we analyzed metatranscriptomic data from the tropical millipede Telodeinopus aoutii at the holobiont level. Functional annotation included identification of expressed CAZymes (CAZy families and EC terms) in the host and its intestinal microbiota, foregut, midgut, and hindgut, compared to non-intestinal tissues. Most of the 175 CAZy families were expressed exclusively in the gut microbiota and more than 50% of these microbial families were expressed exclusively in the hindgut. The greatest diversity of expressed endogenous CAZymes from all gut sections was found in the midgut (77 families). Bacteria were the major microbial producers of CAZymes, Proteobacteria dominating in the midgut and Bacteriodetes with Firmicutes in the hindgut. The contribution of the eukaryotic microbiota to CAZymes production was negligible. Functional classification of expressed CAZy families confirmed a broad functional spectrum of CAZymes potentially expressed in the holobiont. Degradation of lignocellulose in the digestive tract of the millipede T. aoutii depends largely on bacterial enzymes expressed in the hindgut. Endogenous cellulases were not detected, except for the potentially cellulolytic family AA15, but an expression of cellulolytic enzymes of this family was not confirmed at the EC-number level. The midgut had the greatest diversity of expressed endogenous CAZymes, mainly amylases, indicating the importance of digesting α-glucosidases for the millipede. In contrast, bacterial lignocellulolytic enzymes are sparsely expressed here. The hindgut was the hotspot of microbial degradation of cellulose and hemicellulases. The gain of the millipede from the microbial lignocellulose degradation in the gut, and consequently the mutualistic status of the relationship between the millipede and its cellulolytic gut bacteria, depends on the ability of the millipede to take up microbial metabolites as nutrients through the hindgut wall. Enzymes expressed in the intestine can degrade all components of lignocellulose except lignin. Assuming that soil microbiota is partially degraded lignin in the millipede diet, T. aoutii can be considered a decomposer of soil organic matter relying primarily on its gut bacteria. The deposition of millipede fecal pellets containing an organic matter modified by the hindgut bacterial community could be of ecological significance.

Comparative characterization of the hemocyanin-derived phenol oxidase activity from spiders inhabiting different thermal habitats

Enzymes adapted to cold temperatures are commonly characterized for having higher Michaelis-Menten constants (K_M) values and lower optimum and denaturation temperature, when compared to other meso or thermophilic enzymes. Phenoloxidase (PO) enzymes are ubiquitous in nature, however, they have not been reported in spiders. It is the oxygen carrier protein hemocyanin (Hc), found at high concentrations in their hemolymph, which displays an inducible PO activity. Hence, we hypothesize that Hc-derived PO activity could show features of cold adaptation in alpine species. We analyzed the Hc from two species of Theraphosidae from different thermal environments: Euathlus condorito (2400 m a.s.l.) and Grammostola rosea (500 m a.s.l.). Hc was purified from the hemolymph of both spiders and was characterized by identifying subunit composition and measuring the sodium dodecyl sulfate (SDS)-induced PO activity. The high-altitude spider Hc showed higher PO activity under all conditions and higher apparent Michaelis-Menten constant. Moreover, the optimum temperature for PO activity was lower for E. condorito Hc. These findings suggest a potential adaptation at the level of Hc-derived PO activity in Euathlus condorito, giving insights on possible mechanisms used by this mygalomorph spider to occupy extremes and variable thermal environments.

Myriapod haemocyanin: the first three-dimensional reconstruction of Scolopendra subspinipes and preliminary structural analysis of S. viridicornis

Haemocyanins (Hcs) are copper-containing, respiratory proteins that occur in the haemolymph of many arthropod species. Here, we report the presence of Hcs in the chilopode Myriapoda, demonstrating that these proteins are more widespread among the Arthropoda than previously thought. The analysis of transcriptome of S. subspinipes subpinipes reveals the presence of two distinct subunits of Hc, where the signal peptide is present, and six of prophenoloxidase (PPO), where the signal peptide is absent, in the 75 kDa range. Size exclusion chromatography profiles indicate different quaternary organization for Hc of both species, which was corroborated by TEM analysis: S. viridicornis Hc is a 6 × 6-mer and S. subspinipes Hc is a 3 × 6-mer, which resembles the half-structure of the 6 × 6-mer but also includes the presence of phenoloxidases, since the 1 × 6-mer quaternary organization is commonly associated with hexamers of PPO. Studies with Chelicerata showed that PPO activity are exclusively associated with the Hcs. This study indicates that Scolopendra may have different proteins playing oxygen transport (Hc) and PO function, both following the hexameric oligomerization observed in Hcs.

Diversity, evolution, and function of myriapod hemocyanins

Background

Hemocyanin transports O₂ in the hemolymph of many arthropod species. Such respiratory proteins have long been considered unnecessary in Myriapoda. As a result, the presence of hemocyanin in Myriapoda has long been overlooked. We analyzed transcriptome and genome sequences from all major myriapod taxa – Chilopoda, Diplopoda, Symphyla, and Pauropoda – with the aim of identifying hemocyanin-like proteins.

Results

We investigated the genomes and transcriptomes of 56 myriapod species and identified 46 novel full-length hemocyanin subunit sequences in 20 species of Chilopoda, Diplopoda, and Symphyla, but not Pauropoda. We found in Cleidogona sp. (Diplopoda, Chordeumatida) a hemocyanin-like sequence with mutated copper-binding centers, which cannot bind O₂. An RNA-seq approach showed markedly different hemocyanin mRNA levels from ~ 6 to 25,000 reads per kilobase per million reads. To evaluate the contribution of hemocyanin to O₂ transport, we specifically studied the hemocyanin of the centipede Scolopendra dehaani. This species harbors two distinct hemocyanin subunits with low expression levels. We showed cooperative O₂ binding in the S. dehaani hemolymph, indicating that hemocyanin supports O₂ transport even at low concentration. Further, we demonstrated that hemocyanin is > 1500-fold more highly expressed in the fertilized egg than in the adult.

Conclusion

Hemocyanin was most likely the respiratory protein in the myriapod stem-lineage, but multiple taxa may have independently lost hemocyanin and thus the ability of efficient O₂ transport. In myriapods, hemocyanin is much more widespread than initially appreciated. Some myriapods express hemocyanin only at low levels, which are, nevertheless, sufficient for O₂ supply. Notably, also in myriapods, a non-respiratory protein similar to insect storage hexamerins evolved from the hemocyanin.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1221-2) contains supplementary material, which is available to authorized users.

Aerobic respiration by haemocyanin in the embryo of the migratory locust

It remains unresolved how insect embryos acquire sufficient oxygen to sustain high rates of respiratory metabolism during embryogenesis in the absence of a fully developed tracheal system. Our previous work showed that the two distinct subunits (Hc1 and Hc2) of haemocyanin (Hc), a copper-containing protein, display embryo-specific high expression that is essential for embryonic development and survival in the migratory locust Locusta migratoria. Here we investigated the role of haemocyanins in oxygen sensing and supply in the embryo of this locust. Putative binding sites for hypoxia-regulated transcription factors were identified in the promoter region of all of the Hc1 and Hc2 genes. Embryonic expression of haemocyanins was highly upregulated by ambient O₂ deprivation, up to 10-fold at 13% O₂ content. The degree of upregulation of haemocyanins increased with increasing levels of hypoxia. Compared with low-altitude locusts, embryonic expression of haemocyanins in high-altitude locusts from Tibetan plateau was constitutively higher and more robust to oxygen deprivation. These findings strongly suggest an active involvement of haemocyanins in oxygen exchange in embryos. We thus propose a mechanistic model for embryo respiration in which haemocyanin plays a key role by complementing the tracheal system for oxygen transport during embryogenesis.

Gigantism and Its Implications for the History of Life

Gigantism-very large body size-is an ecologically important trait associated with competitive superiority. Although it has been studied in particular cases, the general conditions for the evolution and maintenance of gigantism remain obscure. I compiled sizes and dates for the largest species in 3 terrestrial and 7 marine trophic and habitat categories of animals from throughout the Phanerozoic. The largest species (global giants) in all categories are of post-Paleozoic age. Gigantism at this level appeared tens to hundreds of millions of years after mass extinctions and long after the origins of clades in which it evolved. Marine gigantism correlates with high planktic or seafloor productivity, but on land the correspondence between productivity and gigantism is weak at best. All global giants are aerobically active animals, not gentle giants with low metabolic demands. Oxygen concentration in the atmosphere correlates with gigantism in the Paleozoic but not thereafter, likely because of the elaboration of efficient gas-exchange systems in clades containing giants. Although temperature and habitat size are important in the evolution of very large size in some cases, the most important (and rare) enabling circumstance is a highly developed ecological infrastructure in which essential resources are abundant and effectively recycled and reused, permitting activity levels to increase and setting the stage for gigantic animals to evolve. Gigantism as a hallmark of competitive superiority appears to have lost its luster on land after the Mesozoic in favor of alternative means of achieving dominance, especially including social organization and coordinated food-gathering.