Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis

Abstract

An antibiotic producing novel Planctomycete strain, designated JC280, was isolated from the surface of the plant Hydrilla verticillata collected from an alkaline lake (Buffalo lake), University of Hyderabad, Hyderabad, India. The morphological and chemotaxonomic properties of strain JC280 were in agreement with the characteristics of the genus Planctopirus. The cell shape was spherical to ovoid and some were tear drop shaped. The cells were Gram-stain-negative divided by budding presenting stalks and rosette formation and were non-sporulating. Crateriform structures with a sub-polar flagellum were observed. Characteristic polyamines were putrescine and spermidine. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid (PL1), unidentified glycolipids (GL1-2), an unidentified aminophospholipid (APL), and an unidentified lipid (L3). Major (>10%) fatty acids were C, Cω8c, Cω9c, and summed feature-3. Major (88%) respiratory quinone was MK-6 with minor amount (12%) of MK-7. Strain JC280 showed 99.7% 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776. To resolve their full taxonomic position, the genome sequence was obtained and compared with the available P. limnophila DSM 3776 genome. The genome sequence of strain JC280 was 5,750,243 bp in size with a total of 4490 protein-coding genes, 66 RNA genes, and 2 CRISPR repeats. Based on whole-genome statistics, ANI value, in silico DDH, diversity of secondary metabolite biosynthetic gene clusters, distinct physiological, biochemical and chemotaxonomic differences, strain JC280 represents a new species in the genus Planctopirus, for which the name Planctopirus hydrillae sp. nov. is proposed. The type strain is JC280 (=KCTC 42880 LMG 29153).

Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov.

“…The identity values between strain EC9 T and the Rosistilla oblonga type strain CA51 T are however less clear: while the ANI value of 90.3% is clearly below the accepted species threshold of 95% [ 111 ], the rpoB gene identity of 97.3% and the 16S rRNA gene sequence identity of 99.6% both fall above the proposed species thresholds of 95.5% and 98.7%, respectively [ 80 , 112 ]. In case of the phylum Planctomycetes , it has been shown before that strains often belong to different species according to ANI analysis despite 16S rRNA sequence identities >99% [ 36 , 109 , 113 ]. We therefore assigned strain EC9 T to a separate species based on the ANI value being distinctly below the species threshold, especially as this result was supported by the evaluation of the Rosistilla genomes: while the genomes of the Rosistilla oblonga strains have a very similar DNA G+C content of 58.1% and 58.2%, strain EC9 T has a lower DNA G+C content of 57.9%.…”

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

“…Indeed, Planctomycetes have been found to be associated in close relationships with specific eukaryotes which enable them to expand their physiological capacities. They have been isolated from the giant tiger prawn Penaeus monodon (Fuerst et al, 1997), Posidonia oceanica seagrass (Kohn et al, 2020a), plants (Yadav et al, 2018), cyanobacterial aggregates (Kohn et al, 2016), macroalga Lage and Bondoso, 2014), marine sponges (Pimentel-Elardo et al, 2003;Kohn et al, 2020b;Wiegand et al, 2020), Sphagnum peat bog (Kulichevskaya et al, 2007b;Kulichevskaya et al, 2009), and lichens (Ivanova et al, 2016). Their sequences have been also detected in a termite Coptotermes formosanus gut (Shinzato et al, 2005), in an acidic Sphagnum peat bog (Dedysh et al, 2006), human oral microbiota (Takeshita et al, 2015), human gut microbiota (Cayrou et al, 2013) and from immunocompromised patient's blood (Drancourt et al, 2014).…”

Stieleriacines, N-Acyl Dehydrotyrosines From the Marine Planctomycete Stieleria neptunia sp. nov.

“…Employing comparative genomics, it was shown that the compartmentalization and complex life cycle of Planctomycetes are associated with a sophisticated signal transduction repertoire (Jogler et al, 2012). Their large genomes of up to 12.4 Mb contain a multitude of gene clusters putatively involved in secondary metabolite production (Jeske et al, 2013;Ravin et al, 2018;Yadav et al, 2018). While extracts of various Planctomycetes showed antimicrobial activity (Graça et al, 2016;Jeske et al, 2016) and anticancer effects (Calisto et al, 2019), only very recently the first structures of secondary metabolites from Planctomycetes have been elucidated (Panter et al, 2019;Kallscheuer et al, 2020).…”