A Gram-stain-negative, facultatively anaerobic, gliding, yellow-pigmented bacterium, designated SS12^T, was isolated from shark gill homogenate and characterized using a polyphasic approach. The strain was catalase-positive and oxidase-negative. Optimal growth occurred at 28–30 °C, pH 7.0–7.5 and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The strain contained MK-7 as the prevailing menaquinone; iso-C_15 : 0 and anteiso-C_15 : 0 as the major cellular fatty acids; and phosphatidylethanolamine and an unknown lipid as the predominant polar lipids. Comparative analysis of 16S rRNA gene sequences demonstrated that the novel isolate showed the highest sequence similarity (94.68 %) to Saccharicrinis fermentans DSM 9555^T and the sequence similarities among the type strains of all other species studied were less than 92 %. A phylogenetic tree, based on 16S rRNA gene sequences, showed that strain SS12^T and Saccharicrinis fermentans DSM 9555^T formed a distinct cluster within the family Marinilabiliaceae . On the basis of its phylogenetic position and phenotypic traits, strain SS12^T represents a novel species of genus Saccharicrinis , for which the name Saccharicrinis carchari sp. nov. is proposed. The type strain is SS12^T ( = CICC 10590^T = DSM 27040^T). Emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans are also provided.

The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be “culturable” may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the “uncultured” not only through enriching the abundance of “uncultured,” but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. Considering that cultivation techniques must evolve further—from axenic to mixed cultures—for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.

Background: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.Results: We sampled epiphytic bacteria from specimens ofUlvasp. (green algae),Saccharinasp. (brown algae),Grateloupiasp. andGelidiumsp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.Conclusions: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome.

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.

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22^T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C_15 : 0, anteiso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22^T fell within the class Bacteroidia . Its closest phylogenetic neighbour was the recently described species Draconibacterium orientale , the sole member of the family Draconibacteriaceae , with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family Draconibacteriaceae . The type strain is G22^T ( = CICC 10587^T = DSM 27063^T).

A novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350^T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350^T showed growth on modified nutrient agar supplemented with 0.1 % d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350^T belongs to a novel bacterial order in the class Deltaproteobacteria , and the most closely related type strains belong to the order Desulfuromonadales , with 85.1–85.6 % 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 and iso-C_17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350^T was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class Deltaproteobacteria . Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350^T may represent a novel order of the Deltaproteobacteria . Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350^T. The type strain of Bradymonas sediminis is FA350^T ( = DSM 28820^T = CICC 10904^T); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.