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

Abstract

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

The Complete Protist Symbiont Communities of Coptotermes formosanus and Coptotermes gestroi: Morphological and Molecular Characterization of Five New Species

“…2011) from C. formosanus in China, to which the name H. minor was very recently applied (Nishimura et al. 2020). Cells of H. minor in Japanese termites were identified by fluorescence in situ hybridization (FISH) using probes designed from JN585011 and were reported to average 60 μm in length, similar to the cells we observed, but with a broader range (23–117 μm, n = 497) .…”

“…These cells measured 46.8-86.3 lm in length (mean 64.9 lm, n = 20) and 30.3-69.4 lm in width in broad view (mean 46.6 lm, n = 20). We sequenced 25 clones from five individually isolated cells, all of which formed a moderately supported clade with a previously published sequence (JN585011, published as H. mirabile, Xie et al 2011) from C. formosanus in China, to which the name H. minor was very recently applied (Nishimura et al 2020). Cells of H. minor in Japanese termites were identified by fluorescence in situ hybridization (FISH) using probes designed from JN585011 and were reported to average 60 lm in length, similar to the cells we observed, but with a broader range (23-117 lm, n = 497).…”

“…Nuclei average 9.8 µm wide by 7.4 µm long (7.0-16.7 µm by 5.0-11.8 µm, n = 18), where length is measured along the anterior to posterior axis of the cell, and are positioned anteriorly with a mean distance from the apex of 6.7 µm (3.2-10.4 µm, n = 18). Fixed, fluorescently probed cells matching 18S rRNA sequence JN585011 measured 60 µm in length (23-117 µm, n = 497) and 61 µm in width (24-109 lm, n = 497 cells) (Nishimura et al 2020). Additional representative 18S rRNA gene sequences MN935658-MN935661.…”

“…The 18S rRNA gene has been sequenced for each of these three symbiont species, and a distinct Holomastigotoides-like 18S sequence amplified from whole hindgut DNA suggests there is an additional Holomastigotoides species (Ohkuma et al 2000;Xie et al 2011). While this article was under review, it was named Holomastigotoides minor, because its cells are smaller, on average, than those of H. hartmanni (Nishimura et al 2020). By contrast, only one of the C. gestroi protist symbiont species has been described so far, Pseudotrichonympha leei del Campo & Keeling, and two Cononymphalike 18S rRNA sequences have been obtained from whole hindgut DNA (del Campo et al 2017;Gile et al 2018).…”

“…While this article was under review, it was named Holomastigotoides minor , because its cells are smaller, on average, than those of H. hartmanni (Nishimura et al. 2020). By contrast, only one of the C. gestroi protist symbiont species has been described so far, Pseudotrichonympha leei del Campo & Keeling, and two Cononympha ‐like 18S rRNA sequences have been obtained from whole hindgut DNA (del Campo et al.…”