Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments.

BACKGROUND: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS: Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.

Lutibacter citreus sp. nov., isolated from Arctic surface sediment.

A Gram-stain-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated 1KV19T, was isolated from a surface sediment sample collected near a bay in the Arctic. Growth of strain 1KV19T occurred in 1-4 % (w/v) NaCl (optimum, 2 %), at 4-35 °C (optimum, 25-30 °C) and at pH 6.5-8.0 (optimum, pH 7.0-7.5). The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19T was associated with the genus Lutibacter and had the highest 16S rRNA gene sequence similarity to Lutibacter oceani 325-5T with 98.1 % similarity. Similarity values between strain 1KV19T and the type strains of other Lutibacter species were in the range 95.9-97.6 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain 1KV19T and related species of the genus Lutibacter were 76.4-79.1 and 19.9-22.3 %, respectively. The major cellular fatty acids of strain 1KV19T were iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 1 H. The respiratory quinone was MK-6. The major polar lipids of strain 1KV19T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The phenotypic, genotypic and chemotaxonomic differences between strain 1KV19T and its phylogenetic relatives indicate that strain 1KV19T should be regarded as representing a novel species in the genus Lutibacter, for which the name Lutibacter citreus sp. nov. is proposed. The type strain is 1KV19T (=KCTC 62595T=MCCC 1H00307T).

Marinomonas agarivorans sp. nov., an agar-degrading marine bacterium isolated from red algae.

A Gram-stain-negative, aerobic and curved-rod-shaped bacterium, designated QM202T, was isolated from red algae (Gracilaria blodgettii). Cells of strain QM202T were 0.2-0.3 µm wide and 1.0-2.5 µm long, catalase-negative and oxidase-positive. The strain exhibited an agar-degrading activity. It was motile by means of a single polar flagellum. Optimal growth occurred at 28-30 °C, pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. The DNA G+C content was 41.4 mol%. The isoprenoid quinone was identified as Q-8. Phophatidylethanolamine and phosphatidylglycerol were the predominant phospholipids. The dominant fatty acids were C18:1ω7c, C16:0 and C16:1ω7c and/or iso-C15:0 2-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QM202T belonged to the genus Marinomonas. The closest described neighbour in terms of 16S rRNA gene sequence identity was Marinomonas blandensis MED121T (95.5 %). The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness indicated that strain QM202T can be considered to represent a novel species, Marinomonas agarivorans sp. nov. The type strain is QM202T (=KCTC 52475T=MCCC 1H00145T).

Marinospirillum perlucidum sp. nov., a novel helical bacterium isolated from a sea cucumber culture pond.

Strain F3212T, Gram-stain-negative, aerobic, helical and motile bacterium, was isolated from the marine sediment collected in a sea cucumber culture pond located in Rongcheng, China. Strain F3212T grew optimally at pH 8.5, at 30 °C and in the presence of 3.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain F3212T belongs to the genus Marinospirillum, clustering with M. celere, M. alkaliphilum, M. minutulum, M. megaterium and M. insulare (with 96.4, 94.6, 93.1, 92.4 and 92.1 % 16S rRNA gene sequence similarities, respectively). The chemotaxonomic properties of strain F3212T were similar to those of members of the genus Marinospirillum. Q-8 was the sole respiratory ubiquinone and the genomic DNA G+C content was 53.3 mol%. The major fatty acids were C18 : 1 ω9c, C16 : 0 and C18 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentifed lipid and an unidentified aminophospholipid. The average nucleotide identity scores for strains M. celere DSM 18438T and M. minutulum DSM 6287T were 74.5 and 69.4 %, respectively. The DNA-DNA homologies with M. celere DSM 18438T and M. minutulum DSM 6287T were less than 20 %. It's concluded that strain F3212T represents a new species of the genus Marinospirillum, for which the name Marinospirillum perlucidum sp. nov. is proposed. The type strain is F3212T (=KCTC 52892T=MCCC 1H00198T).

Kineobactrum sediminis gen. nov., sp. nov., isolated from marine sediment.

A novel Gram-stain-negative, rod-shaped marine bacterium, designated strain F02T, was isolated from a marine saltern in Weihai, PR China. The cells of strain F02T were approximately 0.8-1.0×3.0-4.0 µm and motile by means of a polar flagellum. Strain F02T grew optimally at 33-35 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. Strain F02T showed oxidase- and catalase-positive activities. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain F02T belonged to the family Halieaceae and exhibited 16S rRNA gene sequence similarities of 96.6 and 96.4 % to the type strains of Chromatocurvus halotolerans and Parahaliea mediterranea, respectively. The major cellular fatty acids of strain F02T were C18 : 1ω7c, C16 : 1ω7c, C15 : 0 and C18 : 1ω9c. The major polar lipids of strain F02T were phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Strain F02T contained Q-8 as the sole respiratory quinone. The genomic DNA G+C content was 58.4 mol%. The genome sequences of strain F02T and Chromatocurvus halotolerans DSM 23344T had an OrthoANI value of 70.5 %, and the average amino acid identity value between the two genomes was 62.6 %. The sequence similarity value between the rpoB genes of strain F02T and Chromatocurvus halotolerans DSM 23344T was 79.5 %. On the basis of polyphasic analysis, strain F02T represents a novel species in a new genus, for which the name Kineobactrum sediminis gen. nov., sp. nov. is proposed. The type strain is F02T (=KCTC 52616T=MCCC 1H00224T).

Oceanibium sediminis gen. nov., sp. nov., isolated from marine sediment.

A novel Gram-stain-negative, rod-shaped marine bacterium, designated as strain O448T, was isolated from the coastal area of Weihai, China (122° 14' E, 36° 54' N). Cells of strain O448T were non-motile, aerobic, approximately 0.4-0.6 µm wide and 1.5-2.0 µm long. Growth occurred at 20-40 °C (optimally between 33-37 °C), pH 6.5-8.0 (optimally at 7.0) and in the presence of 1.0-5.0 % (w/v) NaCl (optimally between 2.0-3.0 %). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain O448T belongs to family Rhodobacteraceae and exhibits 16S rRNA gene sequence similarities of 94.3, 94.1 and 93.8 % to the type strains of Pontivivens insulae, Halovulum dunhuangense and Maritimibacter alkaliphilus, respectively. The major cellular fatty acid was C18 : 1ω7c and the major polar lipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. Strain O448T contained Q-10 as the sole respiratory quinone. The genomic DNA G+C content was 65.6 mol%. It is evident from phenotypic data and phylogenetic inference that strain O448T represents a novel species in a new genus, for which the name Oceanibiumsediminis gen. nov., sp. nov. is proposed. The type strain is O448T (=KCTC 62076T=MCCC 1H00233T).