Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Design and Experimental Evaluation of a New RNA-FISH Probe to Detect and Identify Paenibacillus sp

Paenibacillus, rod-saped gram-positive endospores forming aerobic or facultative anaerobic bacteria, colonize diverse ecosystems and are involved in the biodegradation of cultural heritage assets. Biodeteriogenic microorganisms can be easily detected/identified by ribonucleic acid- fluorescent in situ hybridization RNA-FISH with specific probes. In this work, probes designed in silico were analyzed to calculate hybridization efficiency and specificity by varying the formamide concentration in the hybridization. The Pab489 probe showed excellent in silico performance with high theoretical maximum efficiency hybridization (99.99%) and specificity and was selected for experimental assays with target Paenibacillus sp. and non-target biodeteriogenic microorganisms. Results assessed by epifluorescence microscopy and flow cytometry revealed that, regardless of the formamide concentration, it was possible to observe that the Pab489-Cy3 probe had a similar signal intensity to the EUB338-Cy3 probe (positive control), so the presence of formamide, a highly toxic and carcinogenic compound used to aid the hybridization process, is not necessary. The designed probe used in FISH assays allows specific in situ identification of Paenibacillus spp. in microbial communities in a culture-independent way. This approach can be employed for screening Paenibacillus spp., showing great potential for future application in biodeterioration of heritage assets, in the search for Paenibacillus strains that produce compounds with biotechnological or medical potential.

Paenibacillus oceani sp. nov., isolated from surface seawater

A Gram-stain-positive and motile bacterial strain, designated IB182363^T, was isolated from surface seawater of the South China Sea. Cells grew at pH 5.0-9.5 (optimum, pH 7.0-8.0), 20-40 °C (optimum, 30 °C) and with 1-8 % (w/v) NaCl (optimum, 2-4 %). On the basis of 16S rRNA gene sequence analysis, strain IB182363^T was affiliated to the genus Paenibacillus and the closest phylogenetically related species was Paenibacillus ginsengarvi DSM18677^T with 96.9 % sequence similarity. The values of whole genome average nucleotide identity analysis and digital DNA-DNA hybridization between the isolate and the closely related type strains were less than 86.3 and 25.6 %, respectively. Chemotaxonomic analysis revealed that strain IB182363^T possessed meso-diaminopimelic acid in the cell-wall peptidoglycan and contained menaquinone MK-7 as the predominant isoprenoid quinone. The major cellular fatty acids were anteiso-C_15 : 0, C_16 : 0 and iso-C_16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, two unidentified aminolipids, two unidentified phospholipids and four unidentified aminophospholipids. The genomic DNA G+C content was 54.5 mol%. On the basis of the above results, strain IB182363^T represents a novel species of the genus Paenibacillus, for which we propose the name Paenibacillus oceani sp. nov. with the type strain IB182363^T (=MCCC 1K04630^T=JCM 34214^T).

Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis

A Gram-stain-positive, rod-shaped, strictly aerobic, endospore-forming and motile bacterium with peritrichous flagella was isolated from a gut sample of the larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Growth was observed at 15-50 °C (optimum, 28-37 °C), pH 6.0-8.0 (pH 7.0) and only without NaCl. 16S rRNA gene sequence comparisons indicated that strain FW100M-2^T had the highest similarity to type strains of Paenibacillus thailandensis S3-4A^T (96.8 %) and Paenibacillus agaridevorans DSM 1355^T (96.3 %), and had sequence similarity values less than 96.0 % to all other taxa. The phylogenetic tree showed that strain FW100M-2^T fell into the genus Paenibacillus, and formed a cluster with P. thailandensis S3-4A^T independent from other Paenibacillus species. Antesio-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0 were detected as the major fatty acids. The only isoprenoid quinone was MK-7. Polar lipids of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified lipid were present. The meso-diaminopimelic acid was present in the cell-wall peptidoglycan. The genomic DNA G+C content was 51.5 mol%. Hence, strain FW100M-2^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus protaetiae sp. nov. is proposed, with FW100M-2^T (=KACC 19327^T=NBRC 113071^T) as the type strain.

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter

A Gram-stain-positive, rod-shaped, non-endospore-forming motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13ar^T was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13ar^T belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88^T (98.5%), Paenibacillus hordei RH-N24^T (98.4%) and Paenibacillus nicotianae YIM h-19^T (98.1%). The major fatty acid was anteiso-C_15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13ar^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13ar^T (= KACC 18728^T = NBRC 112013^T).