Publications

4474

AbstractThe mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single‐molecule real‐time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element‐rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion‐, prophage‐sequences and transposase‐coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage‐specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction‐modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory‐based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.

Anaerobic ammonium oxidation (Anammox) process is a type of biological nitrogen removal technology which is known to directly convert ammonium and nitrite to nitrogen gas. The freshwater ‘Candidatus Kuenenia stuttgartiensis’ anammox under the phylum of Planctomycetes is used to study the parameters that affect the anammox development and the metabolic pathways alongside the associated enzymes. These observations were made using state-of-the art techniques for detecting anammox bacteria based on their small-subunit ribosomal RNA genes, functional genes and unique reaction pathways. This review systematically summarizes up-to-date studies on the parameters affecting the growth of the anammox bacteria and metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome-based predictions. The K. stuttgartiensis survives in summer and winter conditions besides in the aerobic zones (dissolved oxygen >2 mg/L), which consequently contribute to better nitrogen removal in the wastewater treatment. Furthermore, the K. stuttgartiensis utilizes the Wood–Ljungdahl pathway to directly assimilate extracellular formation instead of oxidising it completely to CO2 prior reassimilation.

AbstractCable bacteria of theDesulfobulbaceaefamily are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera:CandidatusElectronema, typically found in freshwater environments, andCandidatusElectrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. To address this, we performed Nanopore long read (total 162.4 Gbp) and Illumina short read (total 148.3 Gbp) shotgun sequencing of selected environmental samples and a single-strain enrichment ofCa. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to nameCa. Electronema halotolerans andCa. Electrothrix laxa, respectively. TheCa. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the “saltwater”Ca. Electrothrix species, indicating howCa. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.

One highly diverse phylogenetic group of Bacteria, Ca . Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya.