Streptomyces zhaozhouensis sp. nov., an actinomycete isolated from candelabra aloe (Aloe arborescens Mill)

Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal

A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.

Genome mining for drug discovery: cyclic lipopeptides related to daptomycin

The cyclic lipopeptide antibiotics structurally related to daptomycin were first reported in the 1950s. Several have common lipopeptide initiation, elongation, and termination mechanisms. Initiation requires the use of a fatty acyl-AMP ligase (FAAL), a free-standing acyl carrier protein (ACP), and a specialized condensation (C^III) domain on the first NRPS elongation module to couple the long chain fatty acid to the first amino acid. Termination is carried out by a dimodular NRPS that contains a terminal thioesterase (Te) domain (CAT-CATTe). Lipopeptide BGCs also encode ABC transporters, apparently for export and resistance. The use of this mechanism of initiation, elongation, and termination, coupled with molecular target-agnostic resistance, has provided a unique basis for robust natural and experimental combinatorial biosynthesis to generate a large variety of structurally related compounds, some with altered or different antibacterial mechanisms of action. The FAAL, ACP, and dimodular NRPS genes were used as molecular beacons to identify phylogenetically related BGCs by BLASTp analysis of finished and draft genome sequences. These and other molecular beacons have identified: (i) known, but previously unsequenced lipopeptide BGCs in draft genomes; (ii) a new daptomycin family BGC in a draft genome of Streptomyces sedi; and (iii) novel lipopeptide BGCs in the finished genome of Streptomyces ambofaciens and the draft genome of Streptomyces zhaozhouensis.

Streptomyces phaeolivaceus sp. nov. and Streptomyces broussonetiae sp. nov., isolated from the leaves and rhizosphere soil of Broussonetia papyrifera

Two novel actinobacteria, designated strains GY16^T and T44^T, were isolated from the leaves and rhizosphere soil of Broussonetia papyrifera, respectively. A polyphasic approach was used for determining their taxonomic position. Results of 16S rRNA gene sequence analysis indicated that strain GY16^T exhibited highest similarities to Streptomyces cinereoruber subsp. fructofermentans CGMCC 4.1593^T (98.82 %), Streptomyces deccanensis KCTC 19241^T (98.76 %), Streptomyces scabiei NRRL B-16523^T (98.69 %), Streptomyces europaeiscabiei KACC 20186^T (98.69 %) and Streptomyces rishiriensis NBRC 13407^T (98.69 %), and strain T44^T showed 99.2, 99.1, 99.1 and <98.7 % sequence similarities to Streptomyces filipinensis CGMCC 4.1452^T, Streptomyces achromogenes subsp. achromogenes DSM 40028^T, Streptomyces durhamensis DSM 40539^T and other Streptomyces species, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GY16^T formed an independent subclade, which indicated that strain GY16^T should belong to a potential novel species; and strain T44^T was closely related to S. filipinensis CGMCC 4.1452^T, S. achromogenes subsp. achromogenes DSM 40028^T, S. durhamensis DSM 40539^T and S. yokosukanensis DSM 40224^T. However, the multilocus sequence analysis evolutionary distance, average nucleotide identity and DNA-DNA hybridization values between closely related relatives were far from the species-level thresholds. In addition, phenotypic and chemotaxonomic characteristics further confirmed that strains GY16^T and T44^T belonged to two distinct species. Based on these results, it is concluded that the isolated strains represent novel species within the genus Streptomyces, for which the names Streptomyces phaeolivaceus sp. nov. (type strain GY16^T=CICC 24807^T=KCTC 49326^T) and Streptomyces broussonetiae sp. nov. (type strain T44^T=CICC 24819^T=JCM 33918^T) are proposed.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat (Triticum aestivum L.)

Two novel Actinobacteria, designated strains NEAU-YY421^T and NEAU-YY642^T, were isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, PR China and characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains NEAU-YY421^T and NEAU-YY642^T belonged to the genus Streptomyces and strain NEAU-YY421^T was most closely related to Streptomyces fumanus CGMCC 4.1732^T (97.9 % sequence similarity) and Streptomyces naganishii DSM 40282^T (97.8 %), and that of strain NEAU-YY642^T to Streptomyces zhaozhouensis LZS-5^T (98.0 %) and Streptomyces sedi YIM 65188^T (97.5 %). The cell walls of the two strains contained ll-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were glucose and ribose. Multilocus sequence analysis using the concatenated sequences of the atp D, gyr B, rec A, rpo B and trp B genes showed that the two strains formed separate branches in the genus Streptomyces. Moreover, a combination of DNA-DNA hybridization results and cultural and physiological properties indicated that the two strains can be distinguished from their closest phylogenetic relatives. Therefore, strains NEAU-YY421^T and NEAU-YY642^T belong to two novel species in the genus Streptomyces, for which the names Streptomyces triticagri sp. nov. (NEAU-YY421^T=CGMCC 4.7476^T=DSM 106775^T) and Streptomyces triticirhizae sp. nov. (NEAU-YY642^T=CCTCC AA 2018092^T=DSM 107172^T) are proposed, respectively.

Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain

Songnen Plain is originally one of the three major glasslands in China and has now become one of the three most concentrated distribution areas of sodic-saline soil worldwide. The soil is continuously degraded by natural and anthropogenic processes, which has a negative impact on agricultural production. The investigation of microbial diversity in this degraded ecosystem is fundamental for comprehending biological and ecological processes and harnessing the potential of microbial resources. The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in saline-alkali soil. The results from this study show that the change in pH under alkaline conditions was not the major contributor in shaping bacterial community in Songnen Plain. The electrical conductivity (EC) content of soil was the most important driving force for bacterial composition (20.83%), and the second most influencing factor was Na⁺ content (14.17%). Bacterial communities were clearly separated in accordance with the EC. The dominant bacterial groups were Planctomycetes, Proteobacteria, and Bacteroidetes among the different salinity soil. As the salt concentration increased, the indicators changed from Planctomycetes and Bacteroidetes to Proteobacteria and Firmicutes. Our results suggest that Proteobacteria and Firmicutes were the main indicator species reflecting changes of the main microbial groups and the EC as a key factor drives the composition of the bacterial community under alkaline conditions in saline-alkali soil of Songnen Plain.

DNA Binding and Molecular Dynamic Studies of Polycyclic Tetramate Macrolactams (PTM) with Potential Anticancer Activity Isolated from a Sponge-Associated Streptomyces zhaozhouensis subsp. mycale subsp. nov

A sponge-associated actinomycete (strain MCCB267) was isolated from a marine sponge Mycale sp. collected in the Indian Ocean off the Southeast coast of India. Phylogenetic studies of this strain using 16S rRNA gene sequencing showed high sequence similarity to Streptomyces zhaozhouensis. However, strain MCCB267 showed distinct physiological and biochemical characteristic features and was thus designated as S. zhaozhouensis subsp. mycale. subsp. nov. A cytotoxicity-guided fractionation of the crude ethyl acetate extract of strain MCCB267 culture medium yielded four pure compounds belonging to the polycyclic tetramate macrolactam (PTM) family of natural products: ikarugamycin (IK) (1), clifednamide A (CF) (2), 30-oxo-28-N-methylikarugamycin (OI) (3), and 28-N-methylikarugamycin (MI) (4). The four compounds exhibited promising cytotoxic activity against NCI-H460 lung carcinoma cells in vitro, by inducing cell death via apoptosis. Flow cytometric analysis revealed that 1, 3, and 4 induced cell cycle arrest during G1 phase in the NCI-H460 cell line, whereas 2 induced cell arrest in the S phase. A concentration-dependent accumulation of cells in the sub-G1 phase was also detected upon treatment of the cancer cell line with compounds 1-4. The in vitro cytotoxicity studies were supported by molecular docking and molecular dynamic simulation analyses. An in silico study revealed that the PTMs can bind to the minor groove of DNA and subsequently induce the apoptotic stimuli leading to cell death. The characterization of the isolated actinomycete, the study of the mode of action of the four PTMs, 1-4, and the molecular docking and molecular dynamic simulations analyses are herein described.

Diversity and Applications of Endophytic Actinobacteria of Plants in Special and Other Ecological Niches

Actinobacteria are wide spread in nature and represent the largest taxonomic group within the domain Bacteria. They are abundant in soil and have been extensively explored for their therapeutic applications. This versatile group of bacteria has adapted to diverse ecological habitats, which has drawn considerable attention of the scientific community in recent times as it has opened up new possibilities for novel metabolites that may help in solving some of the most challenging problems of the day, for example, novel drugs for drug-resistant human pathogens, affordable means to maintain ecological balance in various habitats, and alternative practices for sustainable agriculture. Traditionally, free dwelling soil actinobacteria have been the subject of intensive research. Of late, symbiotic actinobacteria residing as endophytes within the plant tissues have generated immense interest as potential source of novel compounds, which may find applications in medicine, agriculture, and environment. In the light of these possibilities, this review focuses on the diversity of endophytic actinobacteria isolated from the plants of extreme habitats and specific ecological niches. Furthermore, an attempt has been made to assign chemical class to the compounds obtained from endophytic actinobacteria. Potential therapeutic applications of these compounds and the utility of endophytic actinobacteria in agriculture and environment are discussed.

Streptomyces sediminis sp. nov. isolated from crater lake sediment

A novel actinobacterial strain, MKSP12^T, was isolated from coastal sediment of a crater lake in central Anatolia, Turkey. The taxonomic position of the strain was clarified using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MKSP12^T is closely related to Streptomyces specialis GW 41-1564^T with 97.1% sequence similarity. The strain produces aerial hyphae that differentiate into spiral chains of smooth surfaced spores and grows over a temperature range of 20-37 °C, at pH 7-11 and in the presence of 3% (w/v) sodium chloride. The cell wall amino acid is LL-diaminopimelic acid and the whole cell sugars are glucose and ribose. The polar lipids profile consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, two unidentified phospholipids, an unidentified glycophospholipid and eight unidentified glycolipids; iso-C_16:0, iso-C_16:1 G, anteiso-C_17:0 and anteiso-C_17:1 ω9c were identified as the predominant cellular fatty acids (> 10%). Based on morphological and chemotaxonomic characteristics, and phylogenetic analyses, the strain is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces sediminis sp. nov. is proposed with the type strain MKSP12^T (= DSM 100692^T = KCTC 39613^T).

Streptomyces xiangtanensis sp. nov., isolated from a manganese-contaminated soil

An actinomycete strain, designated strain LUSFXJ^T, was isolated from a soil sample obtained near the Xiangtan Manganese Mine, Central-South China and characterised using a polyphasic taxonomic approach. The 16S rRNA gene sequence-based phylogenetic analysis indicated that this strain belongs to the genus Streptomyces. The DNA-DNA relatedness between this strain and two closely related type strains, Streptomyces echinatus CGMCC 4.1642^T and Streptomyces lanatus CGMCC 4.137^T, were 28.7 ± 0.4 and 19.9 ± 2.0%, respectively, values which are far lower than the 70% threshold for the delineation of a novel prokaryotic species. The DNA G+C content of strain LUSFXJ ^T is 75.0 mol%. Chemotaxonomic analysis revealed that the menaquinones of strain LUSFXJ^T are MK-9(H₆), MK-9(H₈), MK-9(H₂) and MK-8(H₈). The polar lipid profile of strain LUSFXJ^T was found to contain diphosphatidylglycerol and an unidentified polar lipid. The major cellular fatty acids were identified as iso-C_15:0, anteiso-C_15:0, iso-C_16:0, C_16:0 and Summed feature 3. Strain LUSFXJ^T was found to contain meso-diaminopimelic acid as the diagnostic cell wall diamino acid and the whole cell hydrolysates were found to be rich in ribose, mannose and glucose. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, it is concluded that strain LUSFXJ^T represents a novel species of the genus Streptomyces, for which the name S. xiangtanensis sp. nov. is proposed. The type strain is LUSFXJ^T (=GDMCC 4.133^T = KCTC 39829^T).

Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil

A novel actinobacterial strain, designated Z1027T, was isolated from a soil sample collected near the Tuotuo River, Qinghai-Tibet Plateau (China). The strain exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus. The taxonomic position of strain Z1027T was determined using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree, together with Streptomyces turgidiscabies ATCC 700248T (99.19 % similarity), Streptomyces graminilatus JL-6T (98.84 %) and Streptomyces reticuliscabiei CFBP 4531T (98.36 %). The genomic DNA G+C content of strain Z1027T was 74±1 mol%. The DNA-DNA relatedness values between strain Z1027T and Streptomyces turgidiscabies ATCC 700248T and Streptomyces reticuliscabiei CFBP 4531T were 38.5±0.4 and 26.2±1.2 %, respectively, both of them significantly lower than 70 %. Chemotaxonomic data revealed that strain Z1027T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, ll-diaminopimelic acid as the diagnostic diamino acid and galactose as a whole-cell sugar. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatydilinositol and seven other unknown polar lipids were detected; iso-C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1027T (=CGMCC 4.7272T=JCM 31054T) should be classified as the type strain of a novel species of the genus Streptomyces,Streptomyces lacrimifluminis sp. nov.

Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus

The novel endophytic actinomycete strain PA1-07T was isolated from the stem of Phyllanthus amarus. The strain displayed the consistent characteristics of members of the genus Streptomyces. The strain produced short spiral spore chains on aerial mycelia. It grew at pH 5-9, at 40 °C and with a maximum of 5 % (w/v) NaCl. It contained ll-diaminopimelic acid, glucose and ribose in the whole-cell hydrolysate. The major cellular menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), while the major cellular fatty acids were C16 : 0, iso-C14 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and four unknown lipids. The DNA G+C content of the strain was 71 mol%. The strain showed the highest 16S rRNA gene sequence similarity with Streptomyces curacoi JCM 4219T (98.77 %). The DNA-DNA relatedness values between strain PA1-07T and S. curacoi JCM 4219T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of these phenotypic and genotypic characteristics, the strain could be distinguished from closely related species of the genus Streptomyces and thus represents a novel species of the genus Streptomyces, for which the name Streptomyces phyllanthi sp. nov. is proposed. The type strain is PA1-07T (=JCM 30865T=KCTC 39785T=TISTR 2346T).

Streptomyces daqingensis sp. nov., isolated from saline-alkaline soil

A novel strain of actinobacteria, designated strain NEAU-ZJC8^T, was isolated from a saline-alkaline soil collected from Heilongjiang Province, north-east China and characterized using a polyphasic approach. Strain NEAU-ZJC8^T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces. Growth occurred at 16-35 °C, pH 5.0-11.0 and in the presence of 0-11 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contained glucose, galactose and ribose. Predominant menaquinones were MK-9(H₆), MK-9(H₄) and MK-9(H₈). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C_16 : 0, iso-C_15 : 0, anteiso-C_17 : 0 and C_16 : 0. The G+C content of the DNA was 72.7 mol%. A phylogenetic tree based on 16S rRNA sequences showed that strain NEAU-ZJC8^T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces haliclonae DSM 41970^T (98.56 % similarity) and Streptomyces marinus NBRC 105047^T (97.96 % similarity). A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ZJC8^T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-ZJC8^T represents a novel species of the genus Streptomyces, for which the name Streptomyces daqingensis sp. nov. is proposed. The type strain is NEAU-ZJC8^T ( = CGMCC 4.7178^T = JCM 30057^T).

A Systemic Review on Aloe arborescens Pharmacological Profile: Biological Activities and Pilot Clinical Trials

Since ancient times, plants and herbal preparations have been used as medicine. Research carried out in the last few decades has verified several such claims. Aloe arborescens Miller, belonging to the Aloe genus (Family Asphodelaceae), is one of the main varieties of Aloe used worldwide. The popularity of the plant in traditional medicine for several ailments (antitumor, immunomodulatory, antiinflammatory, antiulcer, antimicrobial and antifungal activity) focused the investigator's interest on this plant. Most importantly, the reported studies have shown the plant effectiveness on various cancer types such as liver, colon, duodenal, skin, pancreatic, intestinal, lung and kidney types. These multiple biological actions make Aloe an important resource for developing new natural therapies. However, the biological activities of isolated compounds such as glycoprotein, polysaccharides, enzyme and phenolics were insufficient. Considering all these, this contribution provides a systematic review outlining the evidence on the biological efficacy of the plant including the pharmacology and the related mechanisms of action, with specific attention to the various safety precautions, and preclinical and clinical studies, indicating the future research prospects of this plant.

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.

New ikarugamycin derivatives with antifungal and antibacterial properties from Streptomyces zhaozhouensis

A bioassay guided fractionation of the ethyl acetate extract from culture broths of the strain Streptomyces zhaozhouensis CA-185989 led to the isolation of three new polycyclic tetramic acid macrolactams (1-3) and four known compounds. All the new compounds were structurally related to the known Streptomyces metabolite ikarugamycin (4). Their structural elucidation was accomplished using a combination of electrospray-time of flight mass spectrometry (ESI-TOF MS) and 1D and 2D NMR analyses. Compounds 1-3 showed antifungal activity against Aspergillus fumigatus, Candida albicans and antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA).