Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania

Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.

Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0-12.0, 5.0-11.0 and 5.0-11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0-93.1 % average nucleotide identity and 21.3-50.0 % DNA-DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides, for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Taxonomic Identification of the Arctic Strain Nocardioides Arcticus Sp. Nov. and Global Transcriptomic Analysis in Response to Hydrogen Peroxide Stress

Microorganisms living in polar regions rely on specialized mechanisms to adapt to extreme environments. The study of their stress adaptation mechanisms is a hot topic in international microbiology research. In this study, a bacterial strain (Arc9.136) isolated from Arctic marine sediments was selected to implement polyphasic taxonomic identification based on factors such as genetic characteristics, physiological and biochemical properties, and chemical composition. The results showed that strain Arc9.136 is classified to the genus Nocardioides, for which the name Nocardioides arcticus sp. nov. is proposed. The ozone hole over the Arctic leads to increased ultraviolet (UV-B) radiation, and low temperatures lead to increased dissolved content in seawater. These extreme environmental conditions result in oxidative stress, inducing a strong response in microorganisms. Based on the functional classification of significantly differentially expressed genes under 1 mM H2O2 stress, we suspect that Arc9.136 may respond to oxidative stress through the following strategies: (1) efficient utilization of various carbon sources to improve carbohydrate transport and metabolism; (2) altering ion transport and metabolism by decreasing the uptake of divalent iron (to avoid the Fenton reaction) and increasing the utilization of trivalent iron (to maintain intracellular iron homeostasis); (3) increasing the level of cell replication, DNA repair, and defense functions, repairing DNA damage caused by H2O2; (4) and changing the composition of lipids in the cell membrane and reducing the sensitivity of lipid peroxidation. This study provides insights into the stress resistance mechanisms of microorganisms in extreme environments and highlights the potential for developing low-temperature active microbial resources.

Nocardioides ochotonae sp. nov., Nocardioides campestrisoli sp. nov. and Nocardioides pantholopis sp. nov., isolated from the Qinghai-Tibet Plateau

Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313^T, ZJ1307, MC1495^T, Y192, 603^T and X2025) were isolated from the Qinghai-Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides, and strains ZJ1313^T and ZJ1307 were most closely related to N. solisilvae JCM 31492^T (16S rRNA gene sequence similarity, 98.0 %), MC1495^T and Y192 to N. houyundeii 78^T (98.5 %), and 603^T and X2025 to N. dokdonensis JCM 14815^T (97.6 %). The digital DNA-DNA hybridization values of strains ZJ1313^T, MC1495^T and 603^T among each other and with type strains of their closest relatives were all below the 70 % cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C_16 : 0, C_17 : 1  ω8c or C_18 : 1  ω9c. MK-8(H₄) was the predominant respiratory menaquinone and ʟʟ-2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313^T, MC1495^T and 603^T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313^T/ZJ1307, MC1495^T/Y192 and 603^T/X2025 represent three new species of genus Nocardioides, for which the names Nocardioides ochotonae sp. nov. (ZJ1313^T=GDMCC 4.177^T=KCTC 49537^T=JCM 34185^T), Nocardioides campestrisoli sp. nov. (MC1495^T=GDMCC 4.176^T=KCTC 49536^T=JCM 34307^T) and Nocardioides pantholopis sp. nov. (603^T=CGMCC 4.7510^T=DSM 106494^T) are proposed accordingly.

Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai-Tibet Plateau

In the present study, four bacterial strains, two (S-713^T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531^T and 1598) from leaves of dandelion collected on the Qinghai-Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713^T/406 and S-531^T/1598 form two independent branches belonging to the genus Nocardioides, and are closest to Nocardioides lianchengensis, Nocardioides dokdonensis, Nocardioides salarius, Nocardioides marinisabuli, Nocardioides psychrotolerans and Nocardioides szechwanensis. Although sharing MK8-(H₄) as their major isoprenoid quinone, strains S-713^T and S-531^T contained C_18 : 1  ω9c (24.64 and 16.34 %) and iso-C_16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713^T and S-531^T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides, for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713^T (=JCM 33698^T=CGMCC 4.7660^T) and S-531^T (=JCM 33468^T=CGMCC 4.7659^T) as the respective type strains.

Nocardioides antarcticus sp. nov., isolated from marine sediment

Strain M-SA3-94T, an aerobic, Gram-stain-positive, ovoid- to rod-shaped, non-motile bacterium, was isolated from the marine sediment of Ardley cove, King George Island, Antarctica. Strain M-SA3-94T grew optimally at pH 5.0-6.0, 20 °C and in the presence of 1.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain M-SA3-94T belonged to the genus Nocardioides in the family Nocardioidaceae, clustering with Nocardioides plantarum NCIMB 12834T, Nocardioides ginsengagri BX5-10T, Nocardioides marinquilinus CL-GY44T and Nocardioides lianchengensis D94-1T (with 96.1 %, 95.9 %, 94.5 % and 94.7 % 16S rRNA gene sequence similarity, respectively). The chemotaxonomic properties of strain M-SA3-94T were similar to those of members of the genus Nocardioides with validly published names. The major fatty acid was iso-C16 : 0. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol and three unknown phospholipids. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2, 6-diaminopimelic acid. MK-8(H4) was the predominant menaquinone and the DNA G+C content of this strain was 66.7 mol%. On the basis of these phenotypic, phylogenetic and chemotaxonomic data, strain M-SA3-94T represents a novel species of the genus Nocardioides, for which the name Nocardioides antarcticus sp. nov. is proposed. The type strain is M-SA3-94T ( = CCTCC AB2014053T = LMG 28254T).