A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)

The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.

Analysis of the Valgamicin Biosynthetic Pathway Reveals a General Mechanism for Cyclopropanol Formation across Diverse Natural Product Scaffolds

Cyclopropanol rings are highly reactive and may function as molecular "warheads" that affect natural product bioactivity. Yet, knowledge on their biosynthesis is limited. Using gene cluster analyses, isotope labeling, and in vitro enzyme assays, we shed first light on the biosynthesis of the cyclopropanol-substituted amino acid cleonine, a residue in the antimicrobial depsipeptide valgamicin C and the cytotoxic glycopeptide cleomycin A2. We decipher the biosynthetic origin of valgamicin C and show that the cleonine cyclopropanol ring is derived from dimethylsulfoniopropionate (DMSP). Furthermore, we demonstrate that part of the biosynthesis is analogous to the formation of malleicyprol polyketides in pathogenic bacteria. By genome mining and metabolic profiling, we identify the potential to produce cyclopropanol rings in other bacterial species. Our results reveal a general mechanism for cyclopropyl alcohol biosynthesis across diverse natural products that may be harnessed for bioengineering and drug discovery.

Antimicrobial Efficacy of 7-Hydroxyflavone Derived from Amycolatopsis sp. HSN-02 and Its Biocontrol Potential on Cercospora Leaf Spot Disease in Tomato Plants

The actinomycete strain HSN-02 was isolated from the soil of a mining field in the Sandur region, Bellary, Karnataka, India. According to the morphological, cultural, physiological, and biochemical characteristics and the 16S rDNA sequence analysis, the strain HSN-02 was identified as Amycolatopsis sp. The antimicrobial activity strain HSN-02 presented stable and moderate inhibitory activity against human pathogens. In pot experiments in the greenhouse, the development of Cercospora leaf spot was markedly suppressed by treatment with the purified compound from the strain HSN-02, and the control efficacy was 45.04 ± 1.30% in Septoria lycopersici-infected tomato plants. A prominent compound was obtained from the fermentation broth of the strain HSN-02 using column chromatography and HPLC. The chemical structural analyses using UV, FTIR, HR-ESI-MS, and NMR confirmed that the compound produced by the strain HSN-02 is 7-hydroxyflavone. This investigation showed the role which the actinomycete strain can play in controlling leaf spots caused by S. lycopersici to reduce treatments with chemical fungicides.

Genome sequencing and genomic analysis of Amycolatopsis tucumanensis DSM 45259 applicable in gray, red, and nano-biotechnology

Through the years, the genus Amycolatopsis has demonstrated its biotechnological potential. The need to clean up the environment and produce new antimicrobial molecules led to exploit promising bacterial genera such as Amycolatopsis. In this present work, we analyze the genome of the strain Amycolatopsis tucumanensis AB0 previously isolated from copper-polluted sediments. Phylogenomic and comparative analysis with the closest phylogenetic neighbor was performed. Our analysis showed the genetic potential of the strain to deal with heavy metals such as copper and mitigate oxidative stress. In addition, the ability to produce copper oxide nanoparticles and the presence of genes potentially involved in the synthesis of secondary metabolites suggest that A. tucumanensis may find utility in gray, red, and nano-biotechnology. To our knowledge, this is the first genomic analysis of an Amycolatopsis strain with potential for different biotechnological fields.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid

Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis. The PLA-degrading capability of the four strains was investigated by testing their ability to assimilate lactic acid, fragment PLA polymers, and deteriorate PLA films. The strain SNC was the best PLA degrader—it was able to assimilate lactic acid, constitutively cleave PLA, and form a thick and widespread biofilm on PLA film. The activity of this strain extensively eroded the polymer, leading to a weight loss of 36% in one month in mesophilic conditions.

Micromonospora deserti sp. nov., isolated from the Karakum Desert

An isolate, 13K206^T, with typical morphological characteristics of the genus Micromonospora was obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliation of the strain. The strain showed chemotaxonomical properties consistent with its classification in the genus Micromonospora such as meso- and 3-OH-A₂pm in the cell-wall peptidoglycan, xylose in whole-cell hydrolysate and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was closely related to 'Micromonospora spongicola' S3-1^T, Micromonospora nigra DSM 43818^T and Micromonospora yasonensis DS3186^T with sequence similarities of 98.6, 98.5 and 98.4 %, respectively. Digital DNA-DNA hybridization and average nucleotide identity analyses in addition to gyrB gene analysis confirmed the assignment of the strain to a novel species within the genus Micromonospora for which the name Micromonospora deserti sp. nov. is proposed. The type strain is 13K206^T (=JCM 32583^T=DSM 107532^T). The DNA G+C content of the type strain is 72.4 mol%.

Actinobacteria Derived from Algerian Ecosystems as a Prominent Source of Antimicrobial Molecules

Actinobacteria, in particular "rare actinobacteria" isolated from extreme ecosystems, remain the most inexhaustible source of novel antimicrobials, offering a chance to discover new bioactive metabolites. This is the first overview on actinobacteria isolated in Algeria since 2002 to date with the aim to present their potential in producing bioactive secondary metabolites. Twenty-nine new species and one novel genus have been isolated, mainly from the Saharan soil and palm groves, where 37.93% of the most abundant genera belong to Saccharothrix and Actinopolyspora. Several of these strains were found to produce antibiotics and antifungal metabolites, including 17 new molecules among the 50 structures reported, and some of these antibacterial metabolites have shown interesting antitumor activities. A series of approaches used to enhance the production of bioactive compounds is also presented as the manipulation of culture media by both classical methods and modeling designs through statistical strategies and the associations with diverse organisms and strains. Focusing on the Algerian natural sources of antimicrobial metabolites, this work is a representative example of the potential of a closely combined study on biology and chemistry of natural products.

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.

Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach

Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561^T, Amycolatopsis palatopharyngis DSM 44832^T and Amycolatopsis thermalba NRRL B-24845^T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223^T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832^T and Amycolatopsis marina CGMCC4 3568^T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

BACKGROUND

Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.

RESULTS

Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.

CONCLUSIONS

Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils

An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.

Reclassification of Nocardia species based on whole genome sequence and associated phenotypic data

Type strains of 72 validated Nocardia species were phylogenetically analyzed based on the multilocus sequence analysis (MLSA) concatenated atpD-groL1-groL2-recA-rpoA-secY-sodA-ychF. Furthermore, their similarity based on digital DNA-DNA hybridization (dDDH) was calculated. Nocardia soli, Nocardia cummidelens and Nocardia salmonicida, Nocardia nova and Nocardia elegans, Nocardia exalbida and Nocardia gamkensis, and Nocardia coubleae and Nocardia ignorata formed coherent clades, respectively. Moreover, each set showed over 70% relatedness by dDDH and shared common phenotypic characteristics. Therefore, we propose a reclassification of Nocardia soli and Nocardia cummidelens as a later heterotypic synonym of Nocardia salmonicida, Nocardia elegans as a later heterotypic synonym of Nocardia nova, Nocardia gamkensis as a later heterotypic synonym of Nocardia exalbida, and Nocardia coubleae as a later heterotypic synonym of Nocardia ignorata.

Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains

Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new Amycolatopsis strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available Amycolatopsis genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.

Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile

The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5^T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H₄) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5^T (= NCIMB 14970^T = NRRL B-65279^T).

Amycolatopsis cappadoca sp. nov., isolated from soil

An Amycolatopsis strain, designated AG28^T, isolated from a soil sample collected from Acıgöl, Kapadokya, Turkey, was examined using a polyphasic taxonomic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence showed that the strain is closely related to the type strains of Amycolatopsis deserti GY024^T (97.1%), Amycolatopsis taiwanensis 0345 M-7^T (96.9%) and Amycolatopsis pigmentata TT00-43^T (96.9%). Strain AG28^T was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Amycolatopsis. The strain was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The whole cell sugars identified were rhamnose, ribose, arabinose and galactose. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was identified as MK-9(H₄). Major fatty acids (> 10%) were identified as iso-C_15:0, iso-C_16:0 and iso-C_16:0 2OH. Consequently, on the basis of the data from this polyphasic study, it is proposed that strain AG28^T represents a novel Amycolatopsis species for which the name Amycolatopsis cappadoca sp. nov. is proposed. The type strain is AG28^T (= KCTC 39884^T = DSM 104280^T).

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.