Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, “
            <i>Candidatus</i>
            Berkiella cookevillensis” and “
            <i>Candidatus</i>
            Berkiella aquae”

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance.Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species.This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.

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“… 2003 ),‘ Candidatus Berkiella’ (Mehari et al . 2016 ) and ‘ Candidatus Cochliophilus’ (Tsao et al . 2017 ) .…”

Section: Introductionmentioning

confidence: 99%

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Graells

Ishak

Larsson

et al. 2018

FEMS Microbiology Ecology

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“…We have recently described an intracellular endosymbiont isolated from an amoeba, ‘ Ca. B. cookevillensis’ [1, 2]. The bacterium was isolated from an amoeba found in a cooling tower, and is a coccoid bacterium of 1–3 μm diameter [1].…”

Section: Resultsmentioning

confidence: 99%

“…Analysis of the ‘Ca. B. cookevillensis’ genome [2] implicates several putative proteins with eukaryotic-like domains for PKC and CDK phosphorylation, as well as domains involved in caspase-3 activation and recruitment. As mentioned above, Parvovirus-induced breaks can result in leaking of components between compartments.…”

Section: Discussionmentioning

confidence: 99%

“…‘ Ca. B. cookevillensis’ has 26 dot/icm genes with no homologous genes yet identified for icmT, icmN/dotK, icmM/dotJ, or icmX , although there are 7 hypothetical proteins in close proximity to the dot/icm gene cluster [2, 32–36]. Proteins encoded by dot/icm genes form a transport system through which effector molecules are translocated.…”

Section: Discussionmentioning

confidence: 99%

“…‘ Candidatus Berkiella cookevillensis’ has recently been described as a novel bacterium isolated from an amoeba in a biofilm sample from a cooling tower [1, 2]. This bacterium and the closely related bacterium, ‘ Ca.…”

Section: Introductionmentioning

confidence: 99%

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Infection and nuclear interaction in mammalian cells by ‘Candidatus Berkiella cookevillensis’, a novel bacterium isolated from amoebae

et al. 2019

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Background ‘ Candidatus Berkiella cookevillensis’ and ‘ Ca. Berkiella aquae’ have previously been described as intranuclear bacteria of amoebae. Both bacteria were isolated from amoebae and were described as appearing within the nuclei of Acanthamoeba polyphaga and ultimately lysing their host cells within 4 days. Both bacteria are Gammaproteobacteria in the order Legionellales with the greatest similarity to Coxiella burnetii. Neither bacterium grows axenically in artificial culture media. In this study, we further characterized ‘ Ca. B. cookevillensis’ by demonstrating association with nuclei of human phagocytic and nonphagocytic cell lines. Results Transmission electron microscopy (TEM) and confocal microscopy were used to confirm nuclear co-localization of ‘ Ca. B. cookevillensis’ in the amoeba host A. polyphaga with 100% of cells having bacteria co-localized with host nuclei by 48 h. TEM and confocal microscopy demonstrated that the bacterium was also observed to be closely associated with nuclei of human U937 and THP-1 differentiated macrophage cell lines and nonphagocytic HeLa human epithelial-like cells. Immunofluorescent staining revealed that the bacteria-containing vacuole invaginates the nuclear membranes and appears to cross from the cytoplasm into the nucleus as an intact vacuole. Conclusion Results of this study indicate that a novel coccoid bacterium isolated from amoebae can infect human cell lines by associating with the host cell nuclei, either by crossing the nuclear membranes or by deeply invaginating the nuclear membranes. When associated with the nuclei, the bacteria appear to be bound within a vacuole and replicate to high numbers by 48 h. We believe this is the first report of such a process involving bacteria and human cell lines. Electronic supplementary material The online version of this article (10.1186/s12866-019-1457-z) contains supplementary material, which is available to authorized users.

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Bacterial and archaeal symbioses with protists

et al. 2021

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Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms -the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly. ll

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Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, “ Candidatus Berkiella cookevillensis” and “ Candidatus Berkiella aquae”

Abstract: “Candidatus Berkiella cookevillensis” and “Candidatus Berkiella aquae” are obligate intranuclear endosymbionts of freshwater amoebae. Here, we present the draft genome sequences of these two bacteria, with total sizes of 2,990,361 bp and 3,626,027 bp, respectively.

Cited by 3 publications

References 9 publications

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Infection and nuclear interaction in mammalian cells by ‘Candidatus Berkiella cookevillensis’, a novel bacterium isolated from amoebae

Bacterial and archaeal symbioses with protists

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