Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan

Abstract

A novel actinobacterial strain, designated SYSU K20354T, was isolated from a soil sample collected from a karst cave in Shaoguan city, Guangdong province, southern China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K20354T was most closely related to Agromyces humatus JCM 14319T, and shared the highest sequence identity of 98.3 % based on NCBI database. In addition, 2,4-diaminobutyric acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose and ribose. The major isoprenoid quinone was MK-12, while the major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, three unknown glycolipids, three unknown phospholipids and two unknown lipids. The draft genome size of strain SYSU K20354T was 3.96 Mbp with G+C content of 69.7 mol%. Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain SYSU K20354T and A. humatus JCM 14319T were 90.3 and 55.6 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K20354T represents a novel species of the genus Agromyces , for which the name Agromyces cavernae sp. nov. is proposed. The type strain is SYSU K20354T (=KCTC 49499T= CGMCC 4.7691T).

Agromyces silvae sp. nov., Rathayibacter soli sp. nov., and Nocardioides terrisoli sp. nov., Isolated from Soil

“…In strain W11 T , MK-11 (52.8%) and MK-12 (47.2%) were found to be the predominant menaquinones; this result agrees with the findings reported for other members of the genus Agromyces [ 5 , 6 ]. Similarly, in strain SW19 T , MK-12 (65.4%), MK-11 (19.5%), and MK-13 (15.1%) were found to be the primary menaquinones, which is consistent with observations in other species of the genus Rathayibacter [ 2 , 13 ].…”

“…As of the time of writing of this study, Nocardioides accommodates 166 valid species (accession date: March 25, 2024; https://lpsn.dsmz.de/genus/nocardioides ). The members of genera belonging to Actinomycetota have been identified from diverse habitats, such as soil [ 4 ], cave [ 5 ], gut [ 6 ], sediment [ 7 ], fermented foods [ 8 ], wetland [ 9 ], and groundwater [ 10 ]. Several strains belonging to these genera are also derived from plant materials and are widely known as endophytic actinobacteria [ 11 - 14 ].…”