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 present, it is widely believed that a 95-96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA-DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95-96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.

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

A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.

Endophytes and Halophytes to Remediate Industrial Wastewater and Saline Soils: Perspectives from Qatar

Many halophytes are considered to be salt hyperaccumulators, adopting ion extrusion and inclusion mechanisms. Such plants, with high aboveground biomass, may play crucial roles in saline habitats, including soil desalination and phytoremediation of polluted soils and waters. These plants cause significant changes in some of the soil’s physical and chemical properties; and have proven efficient in removing heavy metals and metabolizing organic compounds from oil and gas activities. Halophytes in Qatar, such as Halopeplis perfoliata, Salicornia europaea, Salsola soda, and Tetraena qatarensis, are shown here to play significant roles in the phytoremediation of polluted soils and waters. Microorganisms associated with these halophytes (such as endophytic bacteria) might boost these plants to remediate saline and polluted soils. A significant number of these bacteria, such as Bacillus spp. and Pseudomonas spp., are reported here to play important roles in many sectors of life. We explore the mechanisms adopted by the endophytic bacteria to promote and support these halophytes in the desalination of saline soils and phytoremediation of polluted soils. The possible roles played by endophytes in different parts of native plants are given to elucidate the mechanisms of cooperation between these native plants and the associated microorganisms.

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

Three novel actinomycete strains, designated as DR6-1^T, 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-C_16 : 0 and iso-C_15 : 0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1^T, DR6-2 and DR6-4 shared 99.9-100 % 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831^T (98.7-98.8%). The approximate genome size of strain DR6-1^T was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1^T and Amycolatopsis echigonensis JCM21831^T, Amycolatopsis rubida JCM 10871^T and Amycolatopsis nivea KCTC 39515^T 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 DR6-1^T, 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 DR6-1^T (=JCM 33742^T=KCTC 49546^T=TISTR 2840^T).

Amycolatopsis pittospori sp. nov., an endophytic actinobacterium isolated from native apricot tree and genome mining revealed the biosynthesis potential as antibiotic producer and plant growth promoter

An endophytic actinobacterium, strain PIP199^T, was isolated from a root sample of a native apricot growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. The result of a polyphasic study showed that this strain was identified as a new member of the genus Amycolatopsis. Strain PIP199^T is an aerobic actinobacterium with well-developed substrate mycelia and aerial mycelia that form short chains of spores. Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409^T (99.7%), Amycolatopsis lurida DSM 43134^T (99.6%) and Amycolatopsis keratiniphila subsp. nogabecina DSM 44586^T (99.4%) shared the highest 16S rRNA gene sequence similarity. A. keratiniphila subsp. keratiniphila DSM 44409^T and A. lurida DSM 43134^T were the closest phylogenetic neighbors. Chemotaxonomic data including major fatty acids, cell wall components and major menaquinones confirmed the affiliation of strain PIP199^T to the genus Amycolatopsis. The phylogenetic analysis, physiological and biochemical studies and genomic study, allowed the genotypic and phenotypic differentiation of strain PIP199^T and the closely related species with valid names. ANIb and dDDH values when compared to Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409^T were 87.3% and 36.4%, respectively. The name proposed for the new species is Amycolatopsis pittospori sp. nov. The type strain is PIP199^T (= NRRL B-65536^T = TBRC 10618^T).

Amycolatopsis acididurans sp. nov., isolated from peat swamp forest soil in Thailand

A polyphasic approach was used to describe strain K13G38^T, a novel actinomycete isolated from peat swamp forest soil collected from Surat Thani Province, Thailand. The 16S rRNA gene phylogenetic analysis indicated that the strain belonged to the genus Amycolatopsis and showed the highest sequence similarities to both Amycolatopsis acidiphila JCM 30562^T and Amycolatopsis bartoniae DSM 45807^T (96.8% sequence similarity). Furthermore, strain K13G38^T, which formed extensively branched substrate and aerial mycelia, exhibited chemotaxonomical characteristics of the genus Amycolatopsis which included phospholipid pattern type II and cell-wall chemotype IV. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, two unidentified phospholipids, and an unidentified aminolipid. MK-9(H₄) was a predominant menaquinone of the organism. The major cellular fatty acids were iso-C_16:0, anteiso-C_17:0, and C_16:0. The genomic DNA size of strain K13G38^T was 8.5 Mbp with 69.5 mol% G+C content. On the basis of phenotypic characteristics, overall genomic relatedness index and phylogenetic distinctiveness, strain K13G38^T represents a novel species of the genus Amycolatopsis, for which the name A. acididurans sp. nov. is proposed. The type strain is K13G38^T (=TBRC 12507^T = NBRC 114553^T).