Kaistia algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora

Cogrowth advantage: Intestinal microbiota analysis of Bufo gargarizans and Rana chensinensis

Intestinal microbiota has profound effects on host health and adaptation to environmental changes. Bufo gargarizans and Rana chensinensis coexist in the same habitat and have been paid much attention to economically because of their medicinal value. To date, no comparison of differences between single and mixed populations has been made. In our study, differences in the structure and function of the intestinal microbial of B. gargarizans and R. chensinensis in environments of single-species and mixed-species growth were investigated by high-throughput sequencing. Our results suggest that the cogrowth of B. gargarizans and R. chensinensis could lead to the decrease of the abundance of pathogenic bacteria (Bosea) and the introduction or increase of beneficial bacteria (Kaistia, Cetobacterium and Erysipelatoclostridium). The Tax4Fun-based functional predictions revealed that the level of pathways involved in the metabolism of R. chensinensis in mixed-species aquaria is greatly up-regulated. This study provides useful information for ecologists, ecosystem policy makers and wildlife conservationists to promote more effective conservation measures.

Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.

Establishment of an unfed strain of Paramecium bursaria and analysis of associated bacterial communities controlling its proliferation

The ciliate Paramecium bursaria harbors several hundred symbiotic algae in its cell and is widely used as an experimental model for studying symbiosis between eukaryotic cells. Currently, various types of bacteria and eukaryotic microorganisms are used as food for culturing P. bursaria; thus, the cultivation conditions are not uniform among researchers. To unify cultivation conditions, we established cloned, unfed strains that can be cultured using only sterile medium without exogenous food. The proliferation of these unfed strains was suppressed in the presence of antibiotics, suggesting that bacteria are required for the proliferation of the unfed strains. Indeed, several kinds of bacteria, such as Burkholderiales, Rhizobiales, Rhodospirillales, and Sphingomonadales, which are able to fix atmospheric nitrogen and/or degrade chemical pollutants, were detected in the unfed strains. The genetic background of the individually cloned, unfed strains were the same, but the proliferation curves of the individual P. bursaria strains were very diverse. Therefore, we selected multiple actively and poorly proliferating individual strains and compared the bacterial composition among the individual strains using 16S rDNA sequencing. The results showed that the bacterial composition among actively proliferating P. bursaria strains was highly homologous but different to poorly proliferating strains. Using unfed strains, the cultivation conditions applied in different laboratories can be unified, and symbiosis research on P. bursaria will make great progress.

Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea

A Gram-stain-negative, strictly aerobic, catalase-negative, oxidase-positive and non-motile rod-shaped bacterium, designated strain CrO1^T, was isolated from a freshwater alga Cryptomonas obovoidea in the Nakdong river of South Korea. Colonies of CrO1^T were white, convex and circular and growth was observed at 25-40 °C (optimum, 37 °C) and pH 6.0-9.0 (optimum, pH 7) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). CrO1^T contained C_16 : 0, summed feature 5 (comprising C_18 : 0ante and/or C_18 : 2ω6,9c), C_18 : 0, summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c) and summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c) as the major cellular fatty acids (>5 %) and ubiquinone-8 as the sole respiratory quinone. Phosphatidylethanolamine was detected as the major polar lipid. The DNA G+C content of CrO1^T, calculated from the whole genome sequence was 69.6 mol%. CrO1^T was most closely related to Ramlibacter humi 18x22-1^T with a 97.6 % 16S rRNA sequence similarity and shared less than 97.4 % 16S rRNA sequence similarities with other type strains. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that CrO1^T formed a distinct phyletic lineage within the genus Ramlibacter. On the basis of the results of phenotypic, chemotaxonomic and molecular analysis, CrO1^T clearly represents a novel species of the genus Ramlibacter, for which the name Ramlibacter algicola sp. nov. is proposed. The type strain is CrO1^T (=KACC 19926^T=JCM 33302^T).

Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex

A Gram-stain-negative, strictly aerobic bacterium, designated strain PeD5^T, was isolated from a green alga Pediastrum duplex from the Nakdong river of the Republic of Korea. Cells were non-motile cocci, catalase-negative and oxidase-positive. Growth of PeD5^T was observed at 25-40 °C (optimum, 35 °C) and pH 5.0-10.0 (optimum, pH 7-8), and in the presence of 0-0.25% (w/v) NaCl (optimum, 0%). PeD5^T contained C_16:0, C_18:1ω7c 11-methyl, summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (comprising C_18:1ω7c and/or C_18:1ω6c) as major cellular fatty acids (>5%) and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified aminolipid were detected as major polar lipids. The genomic DNA G+C content of PeD5^T was 71.0 mol%. PeD5^T was most closely related to Roseomonas stagni HS-69^T with a 97.6% 16S rRNA sequence similarity and shared less than 96.3% 16S rRNA sequence similarities with type strains of other species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that PeD5^T formed a phyletic lineage with Roseomonas stagni HS-69^T within the genus Roseomonas. On the basis of results of phenotypic, chemotaxonomic and molecular analysis, strain PeD5^T clearly represents a novel species of the genus Roseomonas, for which the name Roseomonas algicola sp. nov. is proposed. The type strain is PeD5^T (=KACC 19925^T=JCM 33309^T).