Rare Halophilic Nocardiopsis from Algerian Saharan Soils as Tools for Biotechnological Processes in Pharmaceutical Industry.

The Sahara Desert, one of the most extreme ecosystems in the planet, constitutes an unexplored source of microorganisms such as mycelial bacteria. In this study, we investigated the diversity of halophilic actinobacteria in soils collected from five regions of the Algerian Sahara. A total of 23 halophilic actinobacterial strains were isolated by using a humic-vitamin agar medium supplemented with 10% NaCl. The isolated halophilic strains were subjected to taxonomic analysis using a polyphasic approach, which included morphological, chemotaxonomic, physiological (numerical taxonomy), and phylogenetic analyses. The isolates showed abundant growth in CMA (complex medium agar) and TSA (tryptic soy agar) media containing 10% NaCl, and chemotaxonomic characteristics were consistent with their assignment to the genus Nocardiopsis. Analysis of the 16S rRNA sequence of 23 isolates showed five distinct clusters and a similarity level ranging between 98.4% and 99.8% within the Nocardiopsis species. Comparison of their physiological characteristics with the nearest species showed significant differences with the closely related species. Halophilic Nocardiopsis isolated from Algerian Sahara soil represents a distinct phyletic line suggesting a potential new species. Furthermore, the isolated strains of halophilic Nocardiopsis were screened for their antagonistic properties against a broad spectrum of microorganisms by the conventional agar method (agar cylinders method) and found to have the capacity to produce bioactive secondary metabolites. Except one isolate (AH37), all isolated Nocardiopsis showed moderate to high biological activities against Pseudomonas syringae and Salmonella enterica, and some isolates showed activities against Agrobacterium tumefaciens, Serratia marcescens, and Klebsiella pneumoniae. However, no isolates were active against Bacillus subtilis, Aspergillus flavus, or Aspergillus niger. The obtained finding implies that the unexplored extreme environments such as the Sahara contain many new bacterial species as a novel drug source for medical and industrial applications.

Pseudoalteromonas rhizosphaerae sp. nov., a novel plant growth-promoting bacterium with potential use in phytoremediation.

Strain RA15T was isolated from the rhizosphere of the halophyte plant Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). RA15T cells were Gram stain-negative, non-spore-forming, aerobic rods and formed cream-coloured, opaque, mucoid, viscous, convex, irregular colonies with an undulate margin. Optimal growth conditions were observed on tryptic soy agar (TSA) plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 28 °C, although it was able to grow at 4-32 °C and at pH values of 5.0-9.0. The NaCl tolerance range was from 0 to 15 %. The major respiratory quinone was Q8 but Q9 was also present. The most abundant fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 1 ω8c and C16 : 0. The polar lipids profile comprised phosphatidylglycerol and phosphatidylethanolamine as the most abundant representatives. Phylogenetic analyses confirmed the well-supported affiliation of strain RA15T within the genus Pseudoalteromonas, close to the type strains of Pseudoalteromonas neustonica, Pseudoalteromonas prydzensis and Pseudoalteromonas mariniglutinosa. Results of comparative phylogenetic and phenotypic studies between strain RA15T and its closest related species suggest that RA15T could be a new representative of the genus Pseudoalteromonas, for which the name Pseudoalteromonas rhizosphaerae sp. nov. is proposed. The type strain is RA15T (=CECT 9079T=LMG 29860T). The whole genome has 5.3 Mb and the G+C content is 40.4 mol%.

Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes(Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans.

Strain EAR18T was isolated as an endophyte from the roots of a halophyte plant, Arthrocnemum macrostachyum, growing in the Odiel marshes (Huelva, Spain). Cells of strain EAR18T were Gram- stain-negative, motile, non-spore-forming aerobic rods. It grew optimally on tryptic soy agar supplemented with 2.5 % NaCl (w/v), at pH 7 and 30 °C for 48 h. It tolerated NaCl from 0 to 25 % (w/v). It presented Q9 as the major quinone and C19 : 0 cyclo ω8c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified phospholipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EAR18T formed a well-supported clade with species Halomonas zincidurans B6T and Halomonas xinjiangensis TRM 0175T (similarities of 98.3 and 96.1 % respectively). Furthermore, digital DNA-DNA hybridization analysis resulted in values of 20.4 % with H. xinjiangensis TRM 0175T and 35.50 % with H. zincidurans B6T, and ANIb/ANIm results in values of 73.8 %/84.2 % with H. xinjiangensis TRM 0175T and 86.8 %/89.4 % with H. zincidurans B6T. Based on phylogeny and differential phenotypic properties in comparison with its closest related species, strain EAR18T is suggested to represent a new species in the genus Halomonas, for which the name Halomonas radicis sp. nov. is proposed. The type strain is EAR18T (=CECT 9077T=LMG 29859T). The whole genome was sequenced, and it had a total length of 4.6 Mbp and a G+C content of 64.9 mol%.

Genome sequence and comparative analysis of Jiangella alba YIM 61503T isolated from a medicinal plant Maytenus austroyunnanensis.

A draft genome sequence of Jiangella alba YIM 61503T revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503T with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503T and J. muralis DSM 45357T, while indicating a high divergence between J. gansuensis YIM 002T and other Jiangella species. The genome of J. alba YIM 61503T also revealed genes involved in indole-3-acetic acid biosynthesis and an alkylresorcinols gene cluster. Further, detection of phosphotransferase genes in the genome of all Jiangella species indicated that they can uptake and phosphorylate sugars. The presences of TreX-Z, TreS and OtsA-OtsB genes in some of the Jiangella strains also indicated a possible mechanism for their tolerance of high salinity. Besides providing new insights into its genetic features, our results suggested that J. alba YIM 61503T could be a potential strain for further genome mining studies. The release of this genome may, therefore, provide a better prospect for understanding "evolutionary taxonomy" about this genus in future.

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant.

Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464(T) and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia. Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464(T) and CPCC 203448 to the genus Williamsia. The DNA-DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia. The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464(T) ( = DSM 45741(T) = KCTC 29118(T)) as the type strain.

Blastococcus endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata.

A novel endophytic actinobacterium, designated strain YIM 68236(T), was isolated from healthy leaves of Camptotheca acuminata. and characterized by using a polyphasic approach. Cells of this strain occurred singly, in pairs or in tetrads. It grew at 10-45 °C, at pH 5.0-8.0 (optimum pH 7.0) and in the presence of 0-3% (w/v) NaCl. The DNA G+C content was 71.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 68236(T) belongs to the genus Blastococcus. However, it differed from its closest relatives, Blastococcus aggregatus DSM 4725(T), Blastococcus saxobsidens DSM 44509(T) and Blastococcus jejuensis DSM 19597(T) in many phenotypic characteristics. Moreover, the DNA-DNA relatedness values between the novel isolate and the three above-mentioned type strains were 49.0 ± 1.6%, 46.1 ± 3.2% and 39.8 ± 1.5%, respectively. Based on comparative analysis of physiological and chemotaxonomic data, strain YIM 68236(T) represents a novel species of the genus Blastococcus, for which the name Blastococcus endophyticus sp. nov. is proposed. The type strain is YIM 68236(T) ( =CCTCC AA 209045(T) =DSM 45413(T) =KCTC 19998(T)).

Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis.

A novel xylan-degrading actinomycete, strain YIM 61515(T), was isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis. Cells were Gram-positive and non-spore-forming, produced primary branches and formed white to yellowish white colonies on the media tested. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61515(T) was most similar to Promicromonospora aerolata V54A(T) and Promicromonospora vindobonensis V45(T) (99.4 and 99.1% sequence similarity, respectively). The isolate formed a separate lineage in a cluster containing P. aerolata V54A(T). 16S rRNA gene sequence similarity between the isolate and other members of the genus Promicromonospora ranged from 96.3 to 98.4%. Chemotaxonomic data, including major menaquinones, fatty acid compositions and polar lipid profiles, supported the placement of strain YIM 61515(T) in the genus Promicromonospora. DNA-DNA relatedness, physiological and biochemical data showed that strain YIM 61515(T) could be distinguished from members of all known species of the genus Promicromonospora and therefore represented a novel species. The name Promicromonospora xylanilytica sp. nov. is proposed, with YIM 61515(T) (=DSM 21603(T)=CCTCC AA 208046(T)) as type strain.

Glycomyces scopariae sp. nov. and Glycomyces mayteni sp. nov., isolated from medicinal plants in China.

Two actinomycete strains, designated YIM 56256(T) and YIM 61331(T), were isolated from the roots of Scoparia dulcis and Maytenus austroyunnanensis, two Chinese medicinal plants, and their taxonomic status was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Glycomyces. 16S rRNA gene sequence analysis showed that they were closely related to each other and to Glycomyces sambucus E71(T). A battery of physiological characteristics and levels of DNA-DNA relatedness indicated that strains YIM 56256(T) and YIM 61331(T) represent two novel species, clearly different from the related known Glycomyces species. On the basis of the data presented, it is evident that each of these strains represents a novel species of the genus Glycomyces, for which the names Glycomyces scopariae sp. nov. (type strain YIM 56256(T) =KCTC 19158(T) =DSM 44968(T)) and Glycomyces mayteni sp. nov. (type strain YIM 61331(T) =KCTC 19527(T) =CCTCC AA 208004(T)) are proposed.