Uncovering the biodiversity and biosynthetic potentials of rare actinomycetes

Background

Antibiotic resistance is on the rise, and new antibiotic research has slowed in recent years, necessitating the discovery of possibly novel microbial resources capable of producing bioactive compounds. Microbial infections are gaining resistance to existing antibiotics, emphasizing the need for novel medicinal molecules to be discovered as soon as possible. Because the possibilities of isolating undiscovered actinomycetes strains have decreased, the quest for novel products has shifted to rare actinomycetes genera from regular environments or the identification of new species identified in unusual habitats.

Main body of the abstract

The non-streptomyces actinobacteria are known as rare actinomycetes that are extremely difficult to cultivate. Rare actinomycetes are known to produce a variety of secondary metabolites with varying medicinal value. In this review, we reported the diversity of rare actinomycetes in several habitat including soil, plants, aquatic environment, caves, insects and extreme environments. We also reported some isolation methods to easily recover rare Actinobacteria from various sources guided with some procedures to identify the rare Actinobacteria isolates. Finally, we reported the biosynthetic potential of rare actinomycetes and its role in the production of unique secondary metabolites that could be used in medicine, agriculture, and industry. These microbial resources will be of interest to humanity, as antibiotics, insecticides, anticancer, antioxidants, to mention but a few.

Short conclusion

Rare actinomycetes are increasingly being investigated for new medicinal compounds that could help to address existing human health challenges such as newly emerging infectious illnesses, antibiotic resistance, and metabolic disorders. The bioactive secondary metabolites from uncommon actinomycetes are the subject of this review, which focuses on their diversity in different habitats, isolation, identification and biosynthetic potentials.

Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology

The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.

Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.)

An aerobic, non-motile, Gram-stain positive actinomycete, designated strain NEAU-YY211^T, was isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, mid-eastern China, and characterised taxonomically using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain NEAU-YY211^T belongs to the genus Pseudonocardia, showing high similarities with respect to Pseudonocardia ammonioxydans H9^T (99.1%) and Pseudonocardia antitumoralis SCSIO 01299^T (99.0%), respectively. The cell wall was found to contain meso-diaminopimelic acid and the whole cell sugars were identified as arabinose and galactose. The predominant menaquinone of strain NEAU-YY211^T was identified as MK-8(H₄) and the major fatty acids were identified as iso-C_16:0, C_17:1ω8c and iso-C_16:1. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The G+C content of the genomic DNA was determined to be 72.6 mol%. Levels of DNA-DNA relatedness with P. ammonioxydans JCM 12462^T and P. antitumoralis DSM 45322^T were 54.5 ± 3.5% and 49.8 ± 2.5% (mean ± SD), respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate can be distinguished from closely related type strains and thus represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia tritici sp. nov. is proposed. The type strain is NEAU-YY211^T (= DSM 106068^T = CGMCC 4.7474^T).

Pseudonocardia mangrovi sp. nov., isolated from soil

A novel Gram-stain-positive, aerobic actinomycete, designated strain SMC 195^T, was isolated from soil collected from a mangrove forest in Thailand. The strain produced extensively branched substrate and aerial mycelia. The substrate mycelium was fragmented into rod-shaped elements, and spore chains consisting of smooth and rod-shaped spores were formed on the aerial mycelium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SMC 195^T represented a member of the genus Pseudonocardia, and the most closely phylogenetically related species were Pseudonocardia yuanmonensisJCM 18055^T (99.2 % 16S rRNA gene sequence similarity), Pseudonocardia halophobicaNRRL B-16514^T (98.9 %) and Pseudonocardia kujensisNRRL B-24890^T (98.7 %). However, the DNA-DNA relatedness values between SMC 195^Tand the closest phylogenetically related species were significantly below 70 %. The G+C content of the genomic DNA was 74±0.8 mol%. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of arabinose, galactose, glucose, rhamnose and ribose. The menaquinone was MK-8(H4) only. The major cellular fatty acid was the branched fatty acid iso-C16 : 0 (33.6 %). The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids. On the basis of the results from phenotypic, chemotaxonomic and genotypic studies, it is concluded that SMC 195^T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia mangrovi sp. nov. is proposed. The type strain is SMC 195^T (=TBRC 7778^T=NBRC 113150^T).

Diversity and bioprospecting of actinomycete endophytes from the medicinal plants

The endophytic actinomycetes constitute one of the fascinating group of microorganisms associated with a wide range of plant species. The diversity of actinomycetes in plants and their tissue parts is a matter of debate as no consensus are derived between individual studies. Nevertheless, their diversity correlates with the occurrence in plant species harboured in unique regions of biologically diverse areas called "hot spots." Recent advances in the isolation techniques have facilitated the isolation of rare taxa from these environments. The biosynthetic ability of the endophytic actinomycetes has proven beyond doubt that these organisms have the potential to synthesize an array of compounds with novelty in structure and bioactivity and as a result are preferred in the natural product screening programs. In the years to come, the scientific world may await to discover many more novel actinomycete taxa with metabolic diversity and applications in therapeutics.

SIGNIFICANCE AND IMPACT OF THE STUDY

"Endophytes" - the microbes residing in the living tissues of plants are virtually omnipresent. Actinomycete endophytes are diverse in distribution within plant tissues, especially in the roots as they have a close association with the rhizhosphere. An introspection into diversity studies necessitates careful sampling, analysis, and isolation data from the biodiverse and nonbiodiverse regions represented by unique environments. The key to the recovery of novel species and their bioprospection lies in these regions.

Continuing hunt for endophytic actinomycetes as a source of novel biologically active metabolites

Drug-resistant pathogens and persistent agrochemicals mount the detrimental threats against human health and welfare. Exploitation of beneficial microorganisms and their metabolic inventions is most promising way to tackle these two problems. Since the successive discoveries of penicillin and streptomycin in 1940s, numerous biologically active metabolites have been discovered from different microorganisms, especially actinomycetes. In recent years, actinomycetes that inhabit unexplored environments have received significant attention due to their broad diversity and distinctive metabolic potential with medical, agricultural and industrial importance. In this scenario, endophytic actinomycetes that inhabit living tissues of plants are emerging as a potential source of novel bioactive compounds for the discovery of drug leads. Also, endophytic actinomycetes are considered as bio-inoculants to improve crop performance through organic farming practices. Further efforts on exploring the endophytic actinomycetes associated with the plants warrant the likelihood of discovering new taxa and their metabolites with novel chemical structures and biotechnological importance. This mini-review highlights the recent achievements in isolation of endophytic actinomycetes and an assortment of bioactive compounds.

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Pseudonocardia cypriaca sp. nov., Pseudonocardia salamisensis sp. nov., Pseudonocardia hierapolitana sp. nov. and Pseudonocardia kujensis sp. nov., isolated from soil

The taxonomic positions of four novel actinomycetes isolated from soil samples, designated KT2142T, PM2084T, K236T and A4038T, were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Pseudonocardia. Whole-cell hydrolysates of the four strains contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars (cell-wall type IV). Their predominant menaquinone was found to be MK-8(H4). The major fatty acid was iso-C16:0. 16S rRNA gene sequence data supported the classification of the isolates in the genus Pseudonocardia and showed that they formed four distinct branches within the genus. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The four isolates were readily distinguished from one another and from the type strains of species classified in the genus Pseudonocardia based on a combination of phenotypic and genotypic properties. In conclusion, it is proposed that the four isolates be classified in four novel species of the genus Pseudonocardia, for which the names Pseudonocardia cypriaca sp. nov. (type strain KT2142T=KCTC 29067T=DSM 45511T=NRRL B-24882T), Pseudonocardia hierapolitana sp. nov. (type strain PM2084T=KCTC 29068T=DSM 45671T=NRRL B-24879T), Pseudonocardia salamisensis sp. nov. (type strain K236T=KCTC 29100T=DSM 45717T) and Pseudonocardia kujensis sp. nov. (type strain A4038T=KCTC 29062T=DSM 45670T=NRRL B-24890T) are proposed.

Pseudonocardia sediminis sp. nov., isolated from marine sediment

A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141(T), was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1-3% (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Pseudonocardia, showing highest levels of similarity with respect to Pseudonocardia sichuanensis KLBMP 1115(T) (97.1%), Pseudonocardia tetrahydrofuranoxydans K1(T) (97.1%) and Pseudonocardia kunmingensis YIM 63158(T) (97.0%). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA-DNA relatedness with P. tetrahydrofuranoxydans DSM 44239(T) was 42.8 ± 3.5% (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141(T) ( = DSM 45779(T) = JCM 18540(T)).

Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment

An aerobic actinomycete, designated SCSIO 01299T, was isolated from a deep-sea sediment collected from the northern South China Sea at a depth of 3258 m. The isolate was found to be a natural producer of the synthesized antitumour agent deoxynyboquinone and its three new derivatives, pseudonocardians A, B and C. A blast search based on almost-complete 16S rRNA gene sequences showed that strain SCSIO 01299T had high sequence similarities with members of the genus Pseudonocardia . The 16S rRNA gene sequence phylogenetic tree revealed that strain SCSIO 01299T was a member of the genus Pseudonocardia . Phenotypic analysis, chemotaxonomy and DNA–DNA relatedness could readily distinguish the isolate from established members in this genus. It was concluded that strain SCSIO 01299T represents a novel species, for which the name Pseudonocardia antitumoralis sp. nov. is proposed. The type strain is SCSIO 01299T ( = DSM 45322T  = CCTCC M 2011255T).

Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge

A novel actinomycete, designated PA3(T), was isolated from an oil refinery wastewater treatment plant, located in Palos de la Frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247(T). The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H(4)) as the predominant menaquinone and iso-C(16:0) as the major fatty acid, are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247(T) showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3(T) represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3(T) (= CCM 8391(T) = CECT 8030(T)).

Methods for the study of endophytic microorganisms from traditional Chinese medicine plants

Plant endophytes are very numerous and widely distributed in nature, their relationships being described as a balanced symbiotic continuum ranging from mutualism through commensalism to parasitism during a long period of coevolution. Traditional Chinese medicines have played a very important role in disease treatment in China and other Asian countries. Investigations show that these medicinal plants harbor endophytes with different kinds of ecological functions, and some of them have potential to produce bioactive small-molecule compounds. This chapter will focus on the selective isolation methods, the diversity of some endophytes (actinobacteria and fungi) isolated from Traditional Chinese Medicine (TCM) plants, and the bioactive compounds from selected endophytic actinobacteria reported in the past 3 years.

Pseudonocardia artemisiae sp. nov., isolated from surface-sterilized Artemisia annua L

A novel actinomycete strain, designated YIM 63587T, was isolated from surface-sterilized roots of Artemisia annua L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63587T was affiliated to the genus Pseudonocardia. 16S rRNA gene sequence similarities between strain YIM 63587T and type strains of species of the genus Pseudonocardia were 96.6–93.8 %. The diagnostic cell-wall diamino acid in the peptidoglycan layer of strain YIM 63587T was meso-diaminopimelic acid and the whole-cell sugars were arabinose, galactose, mannose and ribose. The predominant menaquinone was MK-8(H4) (97.7 %). The phospholipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol mannosides, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids (>5 %) were iso-C16 : 0 (44.7 %), iso-C14 : 0 (10.3 %), iso-C16 : 1 H (9.8 %) and iso-C15 : 0 (7.7 %). The G+C content of the genomic DNA was 68.2 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain YIM 63587T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia artemisiae sp. nov. is proposed. The type strain is YIM 63587T ( = DSM 45313T = CCTCC AA 208081T).

Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil

Two actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T  = NBRC 105885T  = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T  = NBRC 105886T  = VTCC D9-26T).

Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L

A Gram-positive, aerobic, actinobacterial strain with rod-shaped spores, designated YIM 63158(T), was isolated from the surface-sterilized roots of Artemisia annua L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63158(T) belonged to the genus Pseudonocardia. The closest neighbours were 'Pseudonocardia sichuanensis' KLBMP 1115 (99.9 % 16S rRNA gene sequence similarity), Pseudonocardia adelaidensis EUM 221(T) (99.1 %) and Pseudonocardia zijingensis DSM 44774(T) (98.8 %); sequence similarities to other members of the genus Pseudonocardia ranged from 98.6 to 94.4 %. The chemotaxonomic characteristics, such as the cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the isolate belonged to the genus Pseudonocardia. The G+C content of the genomic DNA was 73.3 mol%. On the basis of physiological, biochemical and chemotaxonomic data, including low DNA-DNA relatedness between the isolate and other members of the genus Pseudonocardia, it is proposed that strain YIM 63158(T) represents a novel species in this genus, with the name Pseudonocardia kunmingensis sp. nov. The type strain is YIM 63158(T) ( = DSM 45301(T)  = CCTCC AA 208078(T)). [corrected].

Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L

A novel isolate, designated strain KLBMP 1115(T) was isolated from the surface-sterilized root of oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Characterization of the isolate was based on a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KLBMP 1115(T) belongs to the phylogenetic cluster of the genus Pseudonocardia and was most closely related to Pseudonocardia adelaidensis EUM 221(T) (98.9%) and Pseudonocardia zijingensis DSM 44774(T) (98.6%), whereas the DNA-DNA relatedness values between strain KLBMP 1115(T) and the two type strains were 47.3 and 39.7%, respectively. Levels of lower similarities to the type strains of other recognized Pseudonocardia species ranged from 94.4 to 98.4%. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-8(H(4)). The major fatty acids of strain KLBMP 1115(T) was iso-C(16:0). The chemotaxonomic properties of strain KLBMP 1115(T) were consistent with those shared by members of the genus Pseudonocardia. On the basis of the phenotypic features and the DNA-DNA hybridization data, strain KLBMP 1115(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia sichuanensis sp. nov. is proposed. The type strain is KLBMP 1115(T) (=KCTC 19781(T) = CCTCC AA 2010002(T)).