Cerasicoccus maritimus sp. nov. and Cerasicoccus frondis sp. nov., two peptidoglycan-less marine verrucomicrobial species, and description of Verrucomicrobia phyl. nov., nom. rev.

Yoon, Jaewoo; Matsuo, Yoshihide; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

doi:10.2323/jgam.56.213

Cited by 17 publications

(9 citation statements)

References 47 publications

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“…It is worth to notice that our phylogenetic and phylogenomic analyses are among of the most taxonomically exhaustive up to date among Verrucomicrobia and resulted coherent with those from previous studies (Yoon et al 2010;Yoon 2011;Kim et al 2015;Parks et al 2018). They also highlight the necessity of systematic revision for some species and taxa (i.e.…”

Section: Endosymbiont Phylogenysupporting

confidence: 89%

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

Serra

Gammuto

Nitla

et al. 2019

Preprint

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In 1991 Margulis defined holobionts as the assemblage of "two or more organisms, members of different species" which remain associate "throughout a significant portion of the life history". In recent times, holobionts have been described among many and far-related groups of living beings, such as plants, algae, insects, corals, and even humans. These studies have arisen an increasing interest in different contexts but, to our knowledge, the holobiont concept has not been applied in taxonomy. Here we propose a new approach to modern taxonomy, aimed to integrate the holobiont concept and genomic and bioinformatic analyses with the classical/morphological tools traditionally used in taxonomy. The inclusion of symbiont morphology, and of mitochondrial and symbiont genomes will allow the discipline to move toward what could become the "next generation taxonomy". As an example of this new paradigm in the characterization of holobionts, we herein provide the taxonomic description of the ciliate protist Euplotes vanleeuwenhoeki sp. nov. (Euplotia, Ciliophora) and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. (Opitutae, Verrucomicrobia). Interestingly, we found that this endosymbiont has an extremely reduced genome (~163 Kbp), which is suggestive of a high integration with the host and represents the first case of such an extreme reduction in Verrucomicrobia, and the first case in a protist host.University of Pisa PRA_2018_63 project (to GP); the Italian Ministry of Education, University and Research (MIUR): Dipartimenti di Eccellenza Program (2018-2022) -

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Section: Endosymbiont Phylogenysupporting

confidence: 89%

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

Serra

Gammuto

Nitla

et al. 2019

Preprint

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“…Kuenenia stuttgartiensis has been shown to be inhibited by lysozyme and penicillin, which both act on PG (Hu et al, 2013). PG had also been detected in some, but not all, verrucomicrobial species investigated (Yoon et al, 2007a,b, 2008a,b, 2010). In agreement, most PG synthesis genes were detected in Verrucomicrobium spinosum and the functionality of at least one of them has been confirmed (McGroty et al, 2013).…”

Section: Introductionmentioning

confidence: 92%

Evolutionary Cell Biology of Division Mode in the Bacterial Planctomycetes-Verrucomicrobia- Chlamydiae Superphylum

2016

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Bacteria from the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum are exceptions to the otherwise dominant mode of division by binary fission, which is based on the interaction between the FtsZ protein and the peptidoglycan (PG) biosynthesis machinery. Some PVC bacteria are deprived of the FtsZ protein and were also thought to lack PG. How these bacteria divide is still one of the major mysteries of microbiology. The presence of PG has recently been revealed in Planctomycetes and Chlamydiae, and proteins related to PG synthesis have been shown to be implicated in the division process in Chlamydiae, providing important insights into PVC mechanisms of division. Here, we review the historical lack of observation of PG in PVC bacteria, its recent detection in two phyla and its involvement in chlamydial cell division. Based on the detection of PG-related proteins in PVC proteomes, we consider the possible evolution of the diverse division mechanisms in these bacteria. We conclude by summarizing what is known and what remains to be understood about the evolutionary cell biology of PVC division modes.

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“…For other strains the presence of typical cellular PG building blocks was not investigated at the time of their description ( Shieh and Jean, 1998 ; Choo et al, 2007 ), leaving open the question whether peptidoglycan exists in verrucomicrobial subdivision 4. Members of this subdivision have been isolated from soil communities and leafs, while most strains originate from aquatic habitats, including freshwater lakes, marine waters and extreme habitats such as hot springs ( Shieh and Jean, 1998 ; Chin et al, 2001 ; Choo et al, 2007 ; Yoon et al, 2007c , 2010 ). Here we describe the targeted isolation of subdivision 4 Verrucomicrobia, using antibiotic agents as selective markers for β-lactam resistant bacteria.…”

Section: Introductionmentioning

confidence: 99%

Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4

et al. 2017

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The cell wall of free-living bacteria consists of peptidoglycan (PG) and is critical for maintenance of shape as dissolved solutes cause osmotic pressure and challenge cell integrity. Surprisingly, the subdivision 4 of the phylum Verrucomicrobia appears to be exceptional in this respect. Organisms of this subdivision are described to be devoid of muramic or diaminopimelic acid (DAP), usually found as components of PG in bacterial cell walls. Here we describe three novel bacterial strains from a freshwater lake, IG15T, IG16bT, and IG31T, belonging to a new genus in the subdivision 4 of Verrucomicrobia which we found to possess PG as part of their cell walls. Biochemical analysis revealed the presence of DAP not only in these novel strains, but also in Opitutus terrae PB90-1T, the closest described relative of strains IG15T, IG16bT, and IG31T. Furthermore, we found that nearly all genes necessary for peptidoglycan synthesis are present in genomes of subdivision 4 members, as well as in the complete genome sequence of strain IG16bT. In addition, we isolated and visualized PG-sacculi for strain IG16bT. Thus, our results challenge the concept of peptidoglycan-less free-living bacteria. Our polyphasic taxonomy approach places the novel strains in a new genus within the family Opitutaceae, for which the name Lacunisphaera gen. nov. is proposed. Strain designations for IG15T, IG16bT and IG31T are Lacunisphaera parvula sp. nov. (=DSM 26814 = LMG 29468), L. limnophila sp. nov. (=DSM 26815 = LMG 29469) and L. anatis sp. nov. (=DSM 103142 = LMG 29578) respectively, with L. limnophila IG16bT being the type species of the genus.

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Cerasicoccus maritimus sp. nov. and Cerasicoccus frondis sp. nov., two peptidoglycan-less marine verrucomicrobial species, and description of Verrucomicrobia phyl. nov., nom. rev.

Cited by 17 publications

References 47 publications

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

Evolutionary Cell Biology of Division Mode in the Bacterial Planctomycetes-Verrucomicrobia- Chlamydiae Superphylum

Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4

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