Halorussus litoreus sp. nov., isolated from the salted brown alga Laminaria

Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil

Six novel halophilic archaeal strains of XZYJT10^T, XZYJ18^T, XZYJT40^T, XZYJT49^T, YCN54^T and LT46^T were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10^T, XZYJ18^T, XZYJT40^T, XZYJT49^T, YCN54^T, LT46^T and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.

Halorussus halobius sp. nov., Halorussus marinus sp. nov. and Halorussus pelagicus sp. nov., isolated from salted brown alga Laminaria

Four halophilic archaeal strains, designated HD8-83T, LYG-36T, DLLS-82 and RC-68T, were isolated from the salted brown alga Laminaria of three different origins (Dalian, Lianyungang, Dalian and Rongcheng) in PR China. All strains had pleomorphic rod cells that were motile, lysed in distilled water, stained Gram-negative, and formed red-pigmented colonies on agar plate (except for DLLS-82, which formed white colonies). Based on phylogenetic analyses of the 16S rRNA genes, strain HD8-83T was closely related to Halorussus litoreus HD8-51T (97.9 % similarity), strain LYG-36T and DLLS-82 to Halorussus rarus TBN4T (94.4 % and 94.7 % similarities, respectively), and strain RC-68T to Halorussus salinus YJ-37-HT (96.9 % similarity). Results of phylogenetic analyses based on rpoB' genes and 728 concatenated single-copy orthologous clusters also showed that these strains formed three different branches and clustered tightly with the Halorussus members. The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values between strains LYG-36T and DLLS-82 were 98.9, 98 and 92.4%, showing that they were different strains of the same species. While those values between the isolates and other Halorussus members were below 84.7, 82.9 and 28.9 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strains HD8-83T, LYG-36T, DLLS-82 and RC-68T represent three novel species of the genus Halorussus for which the names Halorussus halobius sp. nov. (type strain: HD8-83T=CGMCC 1.15334T=JCM 31110T), Halorussus marinus sp. nov. (type strain: LYG-36T=CGMCC 1.13606T=JCM 32952T; reference strain: DLLS-82=CGMCC 1.13604=JCM 32951) and Halorussus pelagicus sp. nov. (type strain: RC-68T=CGMCC 1.13609T=JCM 32953T) are proposed.

Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms

Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88-100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.

Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms

Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation.

Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB' gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales, with average nucleotide identity, amino acid identity and in silico DNA-DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales, for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

Halostella pelagica sp. nov. and Halostella litorea sp. nov., isolated from salted brown alga Laminaria

Three rod-shaped halophilic archaeal strains, DL-M4T, LYG-109 and DLLS-108T, were isolated from the salted brown alga Laminaria produced in different marine areas of PR China. Cells of strains were motile, formed red-pigmented colonies on agar and lysed in distilled water. The three strains grew optimally with 2.6 M NaCl, with 0.05-0.3 M MgCl2, at 37 °C and at pH 7.0-7.5. The results of phylogenetic analyses based on the 16S rRNA and rpoB' genes differentiated these strains into two clusters belonging to the genus Halostella, which currently contains Halostella salina CBA1114T and Halostella limicola LT12T. Strains DL-M4T and LYG-109 formed a single cluster separate from the current two members of Halostella (94.4-95.7 and 90.0-90.9 % similarities, respectively) while strain DLLS-108T had Hsl. salina CBA1114T as its nearest neighbour (97.7-97.8 and 95.9 % similarities, respectively) and was separated from Hsl. limicola LT12T (94.4-95.8 and 93.4 % similarities, respectively). These clusters represented two distinct novel species as indicated by phenotypic characteristics, polar lipid compositions and whole-genome comparisons. Diverse phenotypic characteristics, morphology and growth characteristics, nutrition and miscellaneous biochemical tests differentiate strains DL-M4T, LYG-109, DLLS-108T from Hsl. limicola LT12T and Hsl. salina CBA1114T. Strains DL-M4T and LYG-109 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three unidentified glycolipids, while strain DLLS-108T contained these polar lipids and two unidentified phospholipids. The major respiratory quinones detected in the three isolates were menaquinone MK-8 and MK-8(H2). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the isolated strains and the current two members of Halostella were found to be 79.3-86.6 (ANI) and 22.9-49.8 % (isDDH). All these results showed that the three isolates represent two novel species of the genus Halostella for which the names Halostella pelagica sp. nov. [type strain dl-M4T (=CGMCC 1.13603T=JCM 32954T)] and Halostella litorea sp. nov. [type strain DLLS-108T(=CGMCC 1.13610T=JCM 32955T)] are proposed.

Halorussus halophilus sp. nov., A Novel Halophilic Archaeon Isolated from a Marine Solar Saltern

The halophilic archaeal strain ZS-3^T (= CGMCC 1.12866^T = JCM 30239^T) was isolated from a sediment sample of Zhoushan marine solar saltern, P. R. China. Phylogenetic analyses based on 16S rRNA, rpoB' genes and the concatenation of 738 protein sequences reveal that strain ZS-3^T was related to members of the genus Halorussus. The OrthoANI and in silico DDH values between strain ZS-3^T and the current Halorussus members are much lower than the threshold values proposed as the species boundary (ANI 95-96% and in silico DDH 70%), suggesting that strain ZS-3^T represents a novel species of Halorussus (Halorussus halophilus sp. nov.). Diverse phenotypic characteristics differentiate strain ZS-3^T from current Halorussus members. Since the strain expressed diverse hydrolyzing enzyme activity, its complete genome was sequenced. The genome of strain ZS-3^T was found to be 4,450,731 bp with total GC content of 61.51%, and comprises one chromosome and three plasmids. A total of 4694 protein coding genes, 43 tRNA genes and 6 rRNA genes were predicted. A CRISPR-Cas system was also detected. The genome encodes sixteen putative glycoside hydrolases, nine extracellular proteases, seventeen aminopeptidases, seven carboxypeptidases, one esterase and one nitrite reductase. The exploration of the hydrolase genes may expand our understanding of adapted mechanism of halophilic archaea surviving optimally in hypersaline environments where containing organic matter. Meanwhile, various hydrolyzing enzymes may extend this microorganism for further applications in salt-based fermentation.