Genomic analysis of a halophilic bacterium Nesterenkonia sp. CL21 with ability to produce a diverse group of lignocellulolytic enzymes

Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.

Description of Nesterenkonia aerolata sp. nov., an actinobacterium isolated from air of manufacturing shop in a pharmaceutical factory

During our studies on the microorganism diversity from air of manufacturing shop in a pharmaceutical factory in Shandong province, China, a Gram-stain-positive, aerobic, cocci-shaped bacterium, designated LY-0111T, was isolated from a settling dish. Strain LY-0111T grew at temperature of 10-42 °C (optimum 35 °C), pH of 5.0-10.0 (optimum pH 7.0) and NaCl concentration of 1-12% (optimum 0.5-3%, w/v). Based on the 16S rRNA gene sequence analysis, the strain shared the highest sequence similarities to Nesterenkonia halophila YIM 70179T (96.2%), and was placed within the radiation of Nesterenkonia species in the phylogenetic trees. The genome of the isolate was sequenced, which comprised 2,931,270 bp with G + C content of 66.5%. A supermatrix tree based on the gene set bac120 indicated that LY-0111T was close related to Nesterenkonia xinjiangensis YIM 70097T (16S rRNA gene sequence similarity 95.3%). Chemotaxonomic analysis indicated that the main respiratory quinones were MK-7, MK-8, and MK-9, the predominant cellular fatty acids were anteiso-C15:0 and iso-C15:0, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. According to the phenotypic, chemotaxonomic and phylogenetic features, strain LY-0111T is considered to represent a novel species, for which the name Nesterenkonia aerolata sp. nov. is proposed. The type strain is LY-0111T (= JCM 36375T = GDMCC 1.3945T). In addition, Nesterenkonia jeotgali was proposed as a later synonym of Nesterenkonia sandarakina, according to the ANI (96.8%) and dDDH (72.9%) analysis between them.

The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery

Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.

Nesterenkonia haasae sp. nov., an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain

An alkaliphilic actinobacterial strain, designated Hz 6-5^T, was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.0, and in the presence of 0.5% (w/v) NaCl or 3% (w/v) KCl. It was catalase-positive and oxidase-negative. The isolate had highest 16S rRNA gene sequence similarities to the type strains of the species Nesternkonia natronophila M8^T (98.2%), N. salmonea GY074^T (98.1%), and N. sphaerica GY239^T (97.4%), and the isolate formed a subclade with the type strains of these species in the neighbor-joining tree based on the 16S rRNA gene sequences. The phylogenetic tree based on the phylogenomic analysis also showed the same results. The DNA‒DNA relatedness (DDH) values of isolate Hz 6-5^T with N. natronophila M8^T, N. halophila DSM 16378^T, and N. halobia CGMCC 1.2323^T were 21.2%, 36.5%, and 32.0%, respectively. The characteristic diamino acid of strain Hz 6-5^T was found to be lysine. The respiratory quinones were MK-9, MK-8, MK-7(H₄), MK-7(H₂) and MK-7 and the major cellular fatty acids (> 10%) were anteiso-C_15:0, anteiso-C_17:0 and iso-C_16:0. The polar lipids detected for strain Hz 6-5^T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, and two unidentified phospholipids. The DNA G + C content of isolate Hz 6-5^T was 60.8%. Based on the results of phylogenetic analysis supported by morphological, physiological, chemotaxonomic, and other differentiating phenotypic evidence, strain Hz 6-5^T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia haasae sp. nov. is proposed. The type strain is Hz 6-5^T (=CPCC 205100^T=NBRC 113521^T).