Use of soil actinomycetes for pharmaceutical, food, agricultural, and environmental purposes

In this article, we reviewed the international scientific production of the last years on actinomycetes isolated from soil aiming to report recent advances in using these microorganisms for different applications. The most promising genera, isolation conditions and procedures, pH, temperature, and NaCl tolerance of these bacteria were reported. Based on the content analysis of the articles, most studies have focused on the isolation and taxonomic description of new species of actinomycetes. Regarding the applications, the antimicrobial potential (antibacterial and antifungal) prevailed among the articles, followed by the production of enzymes (cellulases and chitinases, etc.), agricultural uses (plant growth promotion and phytopathogen control), bioremediation (organic and inorganic contaminants), among others. Furthermore, a wide range of growth capacity was verified, including temperatures from 4 to 60 °C (optimum: 28 °C), pH from 3 to 13 (optimum: 7), and NaCl tolerance up to 32% (optimum: 0-1%), which evidence a great tolerance for actinomycetes cultivation. Streptomyces was the genus with the highest incidence among the soil actinomycetes and the most exploited for different uses. Besides, the interest in isolating actinomycetes from soils in extreme environments (Antarctica and deserts, for example) is growing to explore the adaptive capacities of new strains and the secondary metabolites produced by these microorganisms for different industrial interests, especially for pharmaceutical, food, agricultural, and environmental purposes.

Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian

A novel actinomycete, strain HBU206404^T, belonging to the genus Actinokineospora, was isolated from the lakeside soil of Baiyangdian, in China. Cells grew at 9-37 °C (optimum temperature, 28 °C) and pH 6-9 (optimum, pH 7). Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan, and sugars present in whole-cell hydrolysates were arabinose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H₄). The predominant cellular fatty acids (> 5%) of the strain HBU206404^T were iso-C_16:0 (21.5%), iso-C_15:0 (20.3%), C_16:1ω7c/C_16:1ω6c and/or C_16:1ω6c/C_16:1ω7c (15.0%), iso-C_17:0 (8.6%), C_16:0 (7.0%) and C_17:1ω8c (6.9%). The major polar lipids of the strain HBU206404^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, six unknown aminolipids, two unknown aminolipids and an unidentified lipid. The 16S rRNA gene sequence analysis indicated that the strain HBU206404^T was most closely related to Actinokineospora alba KCTC 19294^T (99.58%), but whole-genome comparisons, using average nucleotide identity (ANI) value (91.77%) and digital DNA-DNA hybridization (dDDH) value (60%), confirmed low genome relatedness. Nitrogen metabolism pathway was found in the genome of strain HBU206404^T which haboured nitrate reductase and nitrite reductase. Other phenotypic characteristics, such as ability to hydrolyze substances, enzyme activity, acid production from carbon source, etc., could also distinguish strain HBU206404^T from Actinokineospora alba KCTC 19294^T. On the basis of genetic and phenotypic evidence, strain HBU206404^T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora xionganensis sp. nov. is proposed. The type strain is HBU206404^T (= MCCC 1K04412^T = KCTC 49404^T).

Luteolibacter luteus sp. nov., isolated from stream bank soil

A non-motile, Gram-stain-negative, rod-shaped and yellow-colored bacterium, designated G-1-1-1^T was obtained from soil sampled at Gwanggyo stream bank, Gyeonggi-do, Republic of Korea. Cells were aerobic, catalase positive, grew optimally at 25-30 °C and hydrolysed aesculin and casein. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-1-1-1^T formed a lineage within the genus Luteolibacter. The closest members were Luteolibacter flavescens GKX^T (97.7% sequence similarity) and Luteolibacter arcticus MC 3726^T (97.3%). The sequence similarities with other members of the genus Luteolibacter were ≤ 93.9%. The genome of strain G-1-1-1^T was 6,412,079 bp long with 5176 protein-coding genes. The diagnostic amino acid of cell-wall peptidoglycan of strain G-1-1-1^T was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-9 and the principal polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. The predominant cellular fatty acids were iso-C_14:0, C_16:1 ω9c, C_16:0, C_14:0 and anteiso-C_15:0. The DNA G + C content was 61.0 mol%. The anti-SMASH analysis of whole genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain G-1-1-1^T represents a novel species in the genus Luteobacter, for which the name Luteolibacter luteus sp. nov. is proposed. The type strain is G-1-1-1^T (= KACC 21614^T = NBRC 114341^T).