Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae

Abstract

Members of the major candidate phylum Dependentiae (a.k.a. TM6) are widespread across diverse environments from showerheads to peat bogs; yet, with the exception of two isolates infecting amoebae, they are only known from metagenomic data. The limited knowledge of their biology indicates that they have a long evolutionary history of parasitism. Here, we present Chromulinavorax destructans (Strain SeV1) the first isolate of this phylum to infect a representative from a widespread and ecologically significant group of heterotrophic flagellates, the microzooplankter Spumella elongata (Strain CCAP 955/1). Chromulinavorax destructans has a reduced 1.2 Mb genome that is so specialized for infection that it shows no evidence of complete metabolic pathways, but encodes an extensive transporter system for importing nutrients and energy in the form of ATP from the host. Its replication causes extensive reorganization and expansion of the mitochondrion, effectively surrounding the pathogen, consistent with its dependency on the host for energy. Nearly half (44%) of the inferred proteins contain signal sequences for secretion, including many without recognizable similarity to proteins of known function, as well as 98 copies of proteins with an ankyrin-repeat domain; ankyrin-repeats are known effectors of host modulation, suggesting the presence of an extensive host-manipulation apparatus. These observations help to cement members of this phylum as widespread and diverse parasites infecting a broad range of eukaryotic microbes.

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

“…In that same fish, we found that the SMS contained more Dependentiae (genus) and a taxa characterized as “metagenome” from the class Babeliales. Both of these taxa are possible protist endosymbionts (Pagnier et al, 2015; Yeoh et al, 2016; Deeg et al, 2019).…”

Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

“…At class level this resulted in a higher similarity of the relative abundances of the prokaryotic communities of the columns (Figure 7B), with Gammaproteobacteria as the most abundant group on average. This also revealed the class Babeliae in the phylum Dependentiae, which is often found to be pathogens of diverse aquatic protists (Deeg et al, 2019), to be present throughout the inoculated columns and in the inlet end of the control column receiving untreated water ( Figure 7B) in up to 1.3% relative abundance. On the other hand, when inspecting the heatmap of the most abundant OTUs, just a few are only present in the control columns; Rhodoferax sp.…”

“…Interestingly, this showed that the class Babeliae in the phylum Dependentiae was present throughout the inoculated columns and in the inlet end of the control columns ( Figure 7B). Members of the phylum Dependentiae (previously called TM6) are often found to be pathogens of diverse aquatic protozoa (Delafont et al, 2015;Deeg et al, 2019). Though found to be only a small part of the total bacterial community.…”

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

“…Dependentiae is a candidate bacterial phylum that has been noted for its reduced coding potential, including a depletion in electron transport chain components (McLean et al, 2013;Yeoh et al, 2016). It has been speculated that these characteristics indicate a symbiotic lifestyle, with energy acquired from hosts via ATP/ADP translocases, which has been confirmed experimentally in a few Dependentiae members (Delafont et al, 2015;Pagnier et al, 2015;Deeg et al, 2019). The well-characterized members of the bacterial phylum Tenericutes consist mostly of obligate pathogens with reduced genomes (Moran and Wernegreen, 2000).…”