Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.

Abstract

Three novel actinomycete strains, designated as DR6-1T, DR6-2 and DR6-4, isolated from the roots of Dendrobium heterocarpum Lindl in Thailand were studied using a polyphasic taxonomic approach. The strains grew at 20–37 °C, at pH 5–10 and with 5 % (w/v) NaCl. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and MK-9(H4) was a major menaquinone. Arabinose and galactose were the major sugars in the cell wall. The predominant cellular fatty acids were iso-C16 : 0 and iso-C15 : 0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1T, DR6-2 and DR6-4 shared 99.9–100 % 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831T (98.7-98.8%). The approximate genome size of strain DR6-1T was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1T and Amycolatopsis echigonensis JCM21831T, Amycolatopsis rubida JCM 10871T and Amycolatopsis nivea KCTC 39515T were 90.55, 92.25, 92.60%, and 47.20, 52.10 and 52.50%, respectively. Based on the phenotypic, chemotaxonomic and genotypic characteristics, it has been concluded that strains DR6-1T, DR6-2 and DR6-4 represent a novel species of the genus Amycolatopsis for which the name Amycolatopsis dendrobii sp. nov. is proposed. The type strain is DR6-1T (=JCM 33742T=KCTC 49546T=TISTR 2840T).

New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis

“…At the time of writing, this genus included more than 80 species with validly published and correct names. 1 The members of the genus Amycolatopsis are distributed in various environments such as peat swamp forest soil ( Teo et al, 2020 , 2021 ), deep-sea sediment ( Zhang et al, 2016 ), arid soil ( Tan et al, 2006 ; Zucchi et al, 2012 ; Busarakam et al, 2016 ), plant tissues ( Wang et al, 2020 ; Tedsree et al, 2021 ), animals, and humans ( Labeda et al, 2003 ; Huang et al, 2004 ). In the past 10 years, Amycolatopsis strains have gained widespread attention due to their potential in antibiotic production, bioremediation, bioconversion, and biodegradation processes ( Dávila Costa and Amoroso, 2014 ; Adamek et al, 2018 ).…”

Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers

“…The planta Amycolatopsis species have been discovered inside the tissues of different plant species: A. samaneae recovered from the roots of Samanea saman ( Duangmal et al., 2011 ), and A. jiangsuensis was isolated from the stems of Dendranthema indicum ( Xing et al., 2013 ), A. stemonae isolated from the stems of Stemona sp. ( Klykleung et al., 2015 ), A. anabasis isolated from the roots of Anabasis elatior ( Wang et al., 2020 ), and A. dendrobii isolated from the roots of Dendrobium heterocarpum Lindl ( Tedsree et al., 2021 ). However, their ability to adapt to plants is not fully understood.…”

Amycolatopsis iheyensis sp. nov., isolated from soil on Iheya Island, Japan

“…During the writing of this article, the genus Amycolatopsis comprised 86 species with validly published names (LPSN, www.bacterio.net/amycolatopsis.html). Amycolatopsis can be identified using a combination of chemotaxonomic, genomic, morphological and phylogenetic criteria [4–6]. A key morphological feature for Amycolatopsis species is the production of long chains of aerial and substrate mycelia.…”