Stephens, M. E. | Search bioRxiv

bioRxiv2020

Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts

Different protist species which colonize the hindguts of wood feeding Reticulitermes termites are associated with endosymbiotic bacteria belonging to the genus Endomicrobium. In this study, we focused on the endosymbionts of three protist species from Reticulitermes flavipes, which included Pyrsonympha vertens, Trichonympha agilis, and Dinenympha species II. Since these protist hosts represented members of difference taxa which colonize different niches within the hindguts of their termite hosts, we investigated if these differences translated to differential gene content and expression in their endosymbionts. Following assembly and comparative genome and transcriptome analyses, we discovered that these endosymbionts differed with respect to possible niche specific traits such carbon metabolism. Our analyses supported that genes related to carbon metabolism were acquired by horizontal gene transfer (HGT) from donor taxa which are present in termites hindgut community. In addition, our analyses supported that these endosymbionts have retained and expressed genes related to natural transformation (competence) and recombination. Taken together, the presence of genes acquired by HGT and a putative competence pathway supported that these endosymbionts are not cut-off from gene flow and that competence may be a mechanism by which members of the Endomicrobium can acquire new traits. ImportanceThe composition and structure of wood, which contains cellulose, hemicellulose and lignin, prevents most organisms from using this common food source. Termites are a rare exception among animals, and they rely on a complex microbiome housed in their hindguts to use wood as a source of food. The lower termite R. flavipes houses a variety of protist and prokaryotes that are the key players the disassembly of lignocellulose. In this paper we describe the genomes and the gene expression profiles of five Endomicrobium endosymbionts living inside three different protist species from R. flavipes. Data from these genomes suggest that these Endomicrobium species have different mechanisms for using both carbon and nitrogen. In addition, they harbor genes that may be used to import free DNA from their environment. This process of DNA-uptake may cntribute to the high levels of horizontal gene transfer often seen in the Endomicrobium species.

microbiology↗

bioRxiv2018

Oligotyping Bacterial Symbionts of Hindgut Protists Reveals Complex Population Structures and Transmission Trends in the Termite Reticulitermes flavipes

The hindgut protists of wood-feeding termites are usually colonized by prokaryotic symbionts. Many of the hurdles that have prevented a better understanding of these symbionts arise from variation among protist and termite host species and the inability to maintain prominent community members in culture. These issues have made it difficult to study the fidelity, acquisition, and differences in colonization of protists by bacterial symbionts. In this study, we use high throughput amplicon sequencing of the V4 region of 16S rRNA genes to determine the composition of bacterial communities associated with single protist cells of six protist species, from the genera Pyrsonympha, Dinenympha, and Trichonympha that are present in the hindgut of the termite Reticulitermes flavipes. By analyzing amplicon sequence variants (ASVs), the diversity and distribution of protist-associated bacteria was compared within and across these six different protist species. ASV analysis showed that, in general, each protist genus associated with a distinct community of bacterial symbionts which were conserved across different termite colonies. However, some ASVs corresponding to ectosymbionts (Spirochaetes) were shared between different Dinenympha species and to a lesser extent with Pyrsonympha and Trichonympha hosts. This suggested that certain bacterial symbionts may be cosmopolitan to some degree and perhaps acquired by horizontal transmission. Using a fluorescence-based cell assay, we could observe the horizontal acquisition of surface-bound bacteria. This acquisition was shown to be time-dependent, involve active processes, and was non-random with respect to binding locations on some protists.

microbiology↗