Back from the dead; the curious tale of the predatory cyanobacteriumVampirovibrio chlorellavorus

Abstract

An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic.

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

“…A set of 195 archaeal genomes previously identified as being of high quality (28) were used to establish a set of 144 archaeal-specific marker genes (Table S13) suitable for phylogenetic inference as described previously (49). Briefly, an initial set of 203 Pfam (50) and TIGRFAM (51) genes present exactly once in >90% of the high-quality genome set were identified.…”

Microbial diversity and iron oxidation at Okuoku‐hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations

“…While the Cyanobacteria phylum has traditionally been considered to exclusively contain oxygenic phototrophs, several deepbranching non-phototrophic clades have recently been described within the Cyanobacteria phylum, including Melainabacteria, a sister group to oxygenic Cyanobacteria (i.e., Oxyphotobacteria), as well as deeper-branching clades(Di Rienzi et al, 2013;Johnson et al, 2013b;Ley et al, 2005;Soo, Woodcroft, Parks, Tyson, & Hugenholtz, 2015;Soo et al, 2014). While the Cyanobacteria phylum has traditionally been considered to exclusively contain oxygenic phototrophs, several deepbranching non-phototrophic clades have recently been described within the Cyanobacteria phylum, including Melainabacteria, a sister group to oxygenic Cyanobacteria (i.e., Oxyphotobacteria), as well as deeper-branching clades(Di Rienzi et al, 2013;Johnson et al, 2013b;Ley et al, 2005;Soo, Woodcroft, Parks, Tyson, & Hugenholtz, 2015;Soo et al, 2014).…”

“…of deeply branching non-phototrophic Cyanobacteria clades are a minor but notable component of OHK samples (up to 0.9% abundance). While the Cyanobacteria phylum has traditionally been considered to exclusively contain oxygenic phototrophs, several deepbranching non-phototrophic clades have recently been described within the Cyanobacteria phylum, including Melainabacteria, a sister group to oxygenic Cyanobacteria (i.e., Oxyphotobacteria), as well as deeper-branching clades(Di Rienzi et al, 2013;Johnson et al, 2013b;Ley et al, 2005;Soo, Woodcroft, Parks, Tyson, & Hugenholtz, 2015;Soo et al, 2014). These deep-branching Cyanobacteria-particularly the clades SHA-109 and ML635J-21, which branch basal to all other…”

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

“…The Melainabacteria are an early branching sister group to the Gloeobacter and crown-group Cyanobacteria [10,11,31], and researchers have also interrogated their genomes for insight into the evolution of oxygenic photosynthesis [10-12,31]. Unlike the Gloeobacter , no known Melainabacteria have the potential for photosynthesis [10,11,31].…”

“…The Melainabacteria are an early branching sister group to the Gloeobacter and crown-group Cyanobacteria [10,11,31], and researchers have also interrogated their genomes for insight into the evolution of oxygenic photosynthesis [10-12,31]. Unlike the Gloeobacter , no known Melainabacteria have the potential for photosynthesis [10,11,31]. Therefore, the genes necessary for photosynthesis were either present in the common ancestor of Melainabacteria and Cyanobacteria and then lost in Melainabacteria and related lineages [32] or oxygenic photosynthesis evolved after the divergence of Melainabacteria and crown-group Cyanobacteria [10-12,31].…”