Cultivation of a vampire: ‘Candidatus Absconditicoccus praedator’

Abstract

Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales).Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate-and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at lifelimiting extremes.

Symbiosis between Patescibacteria and Archaea discovered in wastewater-treating bioreactors

“…One major lineage of the domain Bacteria, Patescibacteria (also known as Candidate Phyla Radiation/CPR) [1,2], is a highly diverse group of bacteria, widely inhabiting [3,4] natural and artificial ecosystems [5,6], characterized with small cell/genome size [7] and poor (genomically predicted) abilities to synthesize cellular building blocks [4] suggestive of symbiotic dependency for cell growth. Most members remain uncultured, leaving major knowledge gaps in the range and nature of their symbioses, but several cultivation-based studies have demonstrated host-specific symbiotic/parasitic interactions between Patescibacteria and other bacteria [8][9][10][11]. This pointed towards specialization towards bacteria-bacteria symbioses, especially given parallels with DPANN, an archaeal analog who has only been observed to interact with other archaea [4,12]; however, one study has reported Patescibacteria-eukarya symbiosis [13], indicating that the Patescibacteria host range reaches beyond bacteria.…”

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

“…Consistent with previous studies [30, 34], many of the recovered Patescibacteria MAGs had very small genomes (often ∼1MB or smaller; Table S2) with highly reduced metabolic potential, often lacking detectable genes for synthesis of fatty acids, nucleotides, and most amino acids (Table S6). Gene patterns also suggested that many of the organisms are obligate anaerobes, lacking aerobic respiration, and that they likely form symbiotic or parasitic associations with other microbes, as has been shown for Patescibacteria cultivated thus far from the Absconditabacterales and Saccharibacteria [39, 40, 47, 48].…”

Metabolic Potential of the Superphylum <i>Patescibacteria</i> Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant

“…To date, only a few of its members ( i.e. , phyla Saccharimonadia and Gracilibacteria ) have been cultured ( Soro et al , 2014 ; He et al , 2015 ; Ibrahim et al , 2021 ; Yakimov et al , 2021 ). These bacteria are parasitic on other bacteria for sustenance; however, since most of them cannot be cultured, the mechanisms underlying their existence are unclear.…”

“…Patescibacteria are commonly characterized by a small genome size (approximately 1.0‍ ‍Mbp) ( Lemos et al , 2020 ; Nakai, 2020 ), limited metabolic potential, and fermentation-based metabolism ( Wrighton et al , 2012 , 2014 ; Albertsen et al , 2013 ; Lemos et al , 2020 ). However, the physiology and phylogeny of Patescibacteria have not yet been elucidated in detail, except for some cultures in the phyla Saccharimonadia and Gracilibacteria ( Soro et al , 2014 ; He et al , 2015 ; Moreira et al , 2021 ; Yakimov et al , 2021 ).…”

“…Hanke et al predicted that the terminal codon UGA encodes glycine in Gracilibacteria ( Hanke et al , 2014 ). These bacteria have poor metabolic potential ( Sieber et al , 2019 ), and some strains were reported to be parasitic on their hosts ( Moreira et al , 2021 ; Yakimov et al , 2021 ).…”