Biology subjects

Sobotnik, J.

Publications and source records attributed to Sobotnik, J..

6 recordsLinked to original sources

bioRxiv2022

Termite diet rather than geographical origin determines the microbiome composition and functional genetic structure of nests from South American and African representatives, as revealed by a multiomics approach

Termites represent one of the most important insect groups worldwide due to their key role as plant decomposers and proxy of carbon recycling in the tropical rainforest ecosystems. Besides, high relevance in research has been given to these social insects due to a prominent role as urban pests. However, one of the most fascinating aspects of termites are their defence strategies that prevent the growth of detrimental microbiological strains on their nests. One success factor is the key role of the nest allied microbiome. Understanding how beneficial microbial strains aid termites in pathogen biocontrol strategies could provide us with an enhanced repertoire for fighting antimicrobial resistant strains or mine for genes for bioremediation purposes. We carried out a multiomics approach for dissecting the nest microbiome in a wide range of termite species, covering several feeding habits and three geographical locations at two tropical sides of the Atlantic Ocean, and an African savanna. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, taxonomical profile for bacteria and fungi through amplicon sequencing, and further dive into the genetic repertoire through a metagenomic sequencing approach. Volatile naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We further assessed the apparent differences in terms of bacterial community structure, having found a stronger influence from feeding habits and genera, rather than the geographical location. Lastly, our metagenomic analysis revealed that the gene content provides both soil feeding genera with similar functional profiles, while the wood feeding genus shows a different one. These results seem to be independent of the geographical location, indicating that the nest functional profile is heavily influenced by the diet of the termite inhabiting, building, and maintaining the nest.

microbiology↗

bioRxiv2021

Using ultraconserved elements to reconstruct the termite tree of life

The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/.

evolutionary biology↗

bioRxiv2021

The functional evolution of termite gut microbiota

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 feel this gap and provide a global understanding of the functional evolution of termite gut microbiota. 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 key 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. 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 smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.

evolutionary biology↗

bioRxiv2021

Neoisoptera repetitively colonised Madagascar after the Middle Miocene climatic optimum

Madagascar is home to many endemic plant and animal species owing to its ancient isolation from other landmasses. This unique fauna includes several lineages of termites, a group of insects known for their key role in organic matter decomposition in many terrestrial ecosystems. How and when termites colonised Madagascar remains unknown. In this study, we used 601 mitochondrial genomes, 93 of which were generated from Madagascan samples, to infer the global historical biogeography of Neoisoptera, a lineage containing upwards of 80% of described termite species. Our results indicate that Neoisoptera colonised Madagascar between seven to ten times independently during the Miocene, between 8.4-16.6 Ma (95% HPD: 6.1-19.9 Ma). This timing matches that of the colonization of Australia by Neoisoptera. Furthermore, the taxonomic composition of the Neoisopteran fauna of Madagascar and Australia are strikingly similar, with Madagascar harbouring an additional two lineages absent from Australia. Therefore, akin to Australia, Neoisoptera colonised Madagascar during the global expansion of grasslands, possibly helped by the ecological opportunities arising from the spread of this new biome.

ecology↗

bioRxiv2021

Historical biogeography of early diverging termite lineages (Isoptera: Teletisoptera)

Termites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites (crown-Isoptera) occurred during the earliest Cretaceous, approximately 140 million years ago, suggesting that both vicariance through continental drift and overseas dispersal may have shaped the distribution of early diverging termite lineages. We reconstruct the historical biogeography of three early diverging termite families - Stolotermitidae, Hodotermitidae, and Archotermopsidae - using the nuclear rRNA genes and mitochondrial genomes of 27 samples. Our analyses confirmed the monophyly of Stolotermitidae + Hodotermitidae + Archotermopsidae (clade Teletisoptera), with Stolotermitidae diverging from a monophyletic Hodotermitidae + Archotermopsidae approximately 100.3 Ma (94.3-110.4 Ma, 95% HPD), and with Archotermopsidae paraphyletic to a monophyletic Hodotermitidae. The Oriental Archotermopsis and the Nearctic Zootermopsis diverged 50.8 Ma (40.7-61.4 Ma, 95% HPD) before land connections between the Palearctic region and North America ceased to exist. The African Hodotermes + Microhodotermes diverged from Anacanthotermes, a genus found in Africa and Asia, 32.1 Ma (24.8-39.9 Ma, 95% HPD), and the most recent common ancestor of Anacanthotermes lived 10.7 Ma (7.3-14.3 Ma, 95% HPD), suggesting that Anacanthotermes dispersed to Asia using the land bridge connecting Africa and Eurasia [~]18-20 Ma. In contrast, the common ancestors of modern Porotermes and Stolotermes lived 20.2 Ma (15.7-25.1 Ma, 95% HPD) and 26.6 Ma (18.3-35.6 Ma, 95% HPD), respectively, indicating that the presence of these genera in South America, Africa, and Australia involved over-water dispersals. Our results suggest that early diverging termite lineages acquired their current distribution through a combination of over-water dispersals and dispersal via land bridges. We clarify the classification by resolving the paraphyly of Archotermopsidae, restricting the family to Archotermopsis and Zootermopsis, and elevating Hodotermopsinae (Hodotermopsis) as Hodotermopsidae (status novum).

evolutionary biology↗

bioRxiv2021

Transoceanic voyages of drywood termites (Isoptera: Kalotermitidae) inferred from extant and extinct species

Termites are major decomposers of organic matter in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae, the second-largest termite family, are widely distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes and nuclear ribosomal RNA genes of [~]120 species, about 27% of kalotermitid diversity, including representatives of 22 of the 23 kalotermitid genera. We found that extant kalotermitids shared a common ancestor 81 Mya (72-91 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the [~]40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying that the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for a critical taxonomic revision of the family and for future comparative analyses of Kalotermitidae.

evolutionary biology↗