Chromulinavorax destructans, a pathogenic TM6 bacterium with an unusual replication strategy targeting protist mitochondrion

Abstract

Most of the diversity of microbial life is not available in culture, and as such we lack even a fundamental understanding of the biological diversity of several branches on the tree of life. One branch that is highly underrepresented is the candidate phylum TM6, also known as the Dependentiae. Their biology is known only from reduced genomes recovered from metagenomes around the world and two isolates infecting amoebae, all suggest that they live highly hostassociated lifestyles as parasites or symbionts. Chromulinavorax destructans is an isolate from the TM6/Dependentiae that infects and lyses the abundant heterotrophic flagellate, Spumella elongata. Chromulinavorax destructans is characterized by a high degree of reduction and specialization for infection, so much so it was discovered in a screen for giant viruses. Its 1.2 Mb genome shows no metabolic potential and C. destructans instead relies on extensive transporter system to import nutrients, and even energy in the form of ATP from the host. Accordingly, it replicates in a viral-like fashion, while extensively reorganizing and expanding the host mitochondrion. 44% of proteins contain signal sequences for secretion, which includes many proteins of unknown function as well as 98 copies of ankyrin-repeat domain proteins, known effectors of host modulation, suggesting the presence of an extensive host-manipulation apparatus.

Experimental assessment of marine microbial interactions: from predatory protists promoting bacterial survival to bacterial lysis of the protists

“…Bacteria growing in high densities may form biofilms that are typically more tolerant to antimicrobial agents (41) and may result in cytotoxic effects on protist grazers (22). Other bacteria found within aquatic environments have also been shown to lyse protists (10,20,21,42). Our results generally agree with the findings in these reports that lysis occurs within 3 -4 days of co-cultivation with pathogenic bacteria.…”

“…Our results generally agree with the findings in these reports that lysis occurs within 3 -4 days of co-cultivation with pathogenic bacteria. Similarly to strain-specific grazing of protists (43), predatory bacteria too may display strain-specific lysis of protists (9,42).…”

Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA)

“…Also showing significant abundance increase in zone H was bacterium TM6, a recently nominated pathogen due to the lack of diverse metabolic genes, suggesting a reliance on host by-products (Yeoh et al 2016 ). In a recent study, bacterivorous flagellate Spumella elongate and other protists were shown to be a target species for candidate phyla TM6 bacteria, where cells were infected and lysed (Deeg et al 2018 ). Similarly, filamentous, host reliant and DNA recycling (Starr 2018 ), Saccharibacteria spp (TM7) were highest in zones H. Such interactions may have an impact on the long term structuring of bacteria community composition, especially where distinctive microbes possess capabilities to adapt to change and out-compete more vulnerable species (Matz and Kjelleberg 2005 ).…”

Entities inside one another ‐ a matryoshka doll in biology?

“…However, the nature of most endosymbiotic interactions remains elusive. The intracellular niches that are occupied by endosymbionts are manifold; some examples include the nucleus , the perinuclear space , the endoplasmic reticulum (Vogt, 1992), chloroplasts (Wilcox, 1986) and mitochondria (Sassera et al, 2006;Deeg et al, 2018). In particular, the latter two are great examples for the Matryoshka doll principle, as symbionts acquired relatively recently replicate inside symbionts acquired hundreds of millions of years ago (Fig.…”