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

Streptomyces argyrophyllae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla

Strain Jing01T, a novel actinomycete from rhizosphere soil of Cathaya argyrophylla, was identified using a polyphasic approach. 16S rRNA gene sequence analysis of strain Jing01T revealed that it was a member of the genus Streptomyces and shared 99.03%, 99.03%, 98.96%, 98.89%, 98.83%, 98.82%, 98.76%, 98.74%, 98.73%, 98.69% and 98.68% similarities to Streptomyces rochei NRRL B-2410T, Streptomyces naganishii NBRC 12892T, Streptomyces rubradiris JCM 4955T, Streptomyces anandii NRRL B-3590T, Streptomyces aurantiogriseus NBRC 12842T, Streptomyces mutabilis NBRC 12800T, Streptomyces rameus LMG 20326T, Streptomyces djakartensis NBRC 15409T, Streptomyces bangladeshensis JCM 14924T, Streptomyces andamanensis KCTC 29502T and Streptomyces tuirus NBRC 15617T, respectively. In phylogenetic trees constructed based on 16S rRNA gene sequences, strain Jing01T generated a separate branch at the middle of the clade, suggesting it could be a potential novel species. In phylogenomic tree, strain Jing01T was related to S. rubradiris JCM 4955T. In phylogenetic trees based on the gene sequences of atpD, gyrB, recA, rpoB and trpB, strain Jing01T was related to S. bangladeshensis JCM 14924T and S. rubradiris JCM 4955T. Whereas, the multilocus sequence analysis distance, average nucleotide identity and DNA-DNA hybridization values between them were much less than the species-level thresholds. This conclusion was further supported by phenotypic and chemotaxonomic analysis. Consequently, strain Jing01T represents a new Streptomyces species, for which the proposed name is Streptomyces argyrophyllae sp. nov. The type strain is Jing01T (= MCCC 1K05707T = JCM 35923T).

Isoptericola croceus sp. nov., a novel actinobacterium isolated from saline-alkali soil

A novel actinomycete, designated strain q2^T, was isolated from the saline-alkaline soil, collected from Daqing, Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain q2^T belongs to the genus Isoptericola, and showed the highest sequence similarity to Isoptericola halotolerans KCTC 19046^T (98.48%) and Isoptericola chiayiensis KCTC 19740^T (98.13%), respectively. The average nucleotide identity values between strain q2^T and other members of the genus Isoptericola were lower than 95% recommended for distinguishing novel prokaryotic species. Cells of strain q2^T were Gram-staining-positive, aerobic, non-motile, rod-shaped and non-spore-forming. Colonies of strain q2^T were golden-yellow pigmented, tidy edged and smooth surfaced. Growth occurred at 15-37 °C (optimum, 29 °C), pH 7.0-10.0 (optimum, pH 8.0). The predominant respiratory quinones were MK-9(H₄) and MK-9(H₂). The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside. The peptidoglycan compositions were L-alanine, D-aspartic, L-glutamic acid and L-lysine (type A4α). The major cellular fatty acids (> 10%) were anteiso-C_15:0, iso-C_15:0, and anteiso-C_17:0. The G+C content of the genomic DNA was determined to be 69.7%. Based on the phenotypic, physiological, genotypic, and phylogenetic data, strain q2^T represents a novel species of the genus Isoptericola, for which the name Isoptericola croceus sp. nov. is proposed. The type strain is q2^T (= GDMCC 1.2923^T = KCTC 49759^T).

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

Bioactive Natural Products in Actinobacteria Isolated in Rainwater From Storm Clouds Transported by Western Winds in Spain

Actinobacteria are the main producers of bioactive natural products essential for human health. Although their diversity in the atmosphere remains largely unexplored, using a multidisciplinary approach, we studied here 27 antibiotic producing Actinobacteria strains, isolated from 13 different precipitation events at three locations in Northern and Southern Spain. Rain samples were collected throughout 2013-2016, from events with prevailing Western winds. NOAA HYSPLIT meteorological analyses were used to estimate the sources and trajectories of the air-mass that caused the rainfall events. Five-day backward air masses trajectories of the diverse events reveals a main oceanic source from the North Atlantic Ocean, and in some events long range transport from the Pacific and the Arctic Oceans; terrestrial sources from continental North America and Western Europe were also estimated. Different strains were isolated depending on the precipitation event and the latitude of the sampling site. Taxonomic identification by 16S rRNA sequencing and phylogenetic analysis revealed these strains to belong to two Actinobacteria genera. Most of the isolates belong to the genus Streptomyces, thus increasing the number of species of this genus isolated from the atmosphere. Furthermore, five strains belonging to the rare Actinobacterial genus Nocardiopsis were isolated in some events. These results reinforce our previous Streptomyces atmospheric dispersion model, which we extend herein to the genus Nocardiopsis. Production of bioactive secondary metabolites was analyzed by LC-UV-MS. Comparative analyses of Streptomyces and Nocardiopsis metabolites with natural product databases led to the identification of multiple, chemically diverse, compounds. Among bioactive natural products identified 55% are antibiotics, both antibacterial and antifungal, and 23% have antitumor or cytotoxic properties; also compounds with antiparasitic, anti-inflammatory, immunosuppressive, antiviral, insecticidal, neuroprotective, anti-arthritic activities were found. Our findings suggest that over time, through samples collected from different precipitation events, and space, in different sampling places, we can have access to a great diversity of Actinobacteria producing an extraordinary reservoir of bioactive natural products, from remote and very distant origins, thus highlighting the atmosphere as a contrasted source for the discovery of novel compounds of relevance in medicine and biotechnology.

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.

Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2

Diseases caused by Sclerotinia sclerotiorum have caused severe losses of many economically important crops worldwide. Due to the long-term persistence of sclerotia in soil and the production of air-borne ascospores, synthetic fungicides play limited roles in controlling the diseases. The application of antagonistic microorganisms can effectively reduce the number of sclerotia and eventually eradicate S. sclerotiorum from soil, and therefore considerable interest has been focused on biological control. Streptomyces sp. NEAU-S7GS2 was isolated from the root of Glycine max and its rhizosphere soil. It showed significant inhibitory activity against the mycelial growth of S. sclerotiorum (99.1%) and completely inhibited sclerotia germination. Compared to the control, in the pot experiment the application of NEAU-S7GS2 not only demonstrated excellent potential to control sclerotinia stem rot of soybean with 77 and 38% decrease in disease incidence and disease index, respectively, but could promote the growth of soybean. The light microscopy and scanning electron microscopy showed that co-culture of NEAU-S7GS2 with S. sclerotiorum on potato dextrose agar could lead to contorted and fragmented mycelia of S. sclerotiorum, which was associated with the secretion of hydrolytic glucanase and cellulase and the production of active secondary metabolites by NEAU-S7GS2. The plant growth promoting activity of NEAU-S7GS2 was related to the solubilization of inorganic phosphate, and production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase and indole acetic acid (IAA). To further explore the plant growth promoting and antifungal mechanisms, the complete genome of strain NEAU-S7GS2 was sequenced. Several genes associated with ammonia assimilation, phosphate solubilization and IAA synthesis, together with genes encoding ACC deaminase, glucanase and α-amylase, were identified. AntiSMASH analysis led to the identification of four gene clusters responsible for the biosynthesis of siderophores including desferrioxamine B and enterobactin. Moreover, the biosynthetic gene clusters of lydicamycins, phenazines, and a glycosylated polyol macrolide showing 88% gene similarity to PM100117/PM100118 were identified. These results suggested that strain NEAU-S7GS2 may be a potential biocontrol agent and biofertilizer used in agriculture.

Arthrobacter silvisoli sp. nov., isolated from forest soil

A novel Gram-stain-positive, strictly aerobic strain, NEAU-SA1^T, which showed a rod-coccus growth life cycle, was isolated from forest soil from Zhangjiajie, Hunan Province, China. The isolate grew at 10-40 °C (optimum 28 °C), at pH 5.0-10.0 (optimum pH 7.0) and in the presence of up to 5 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-SA1^T belonged to the genus Arthrobacter and was closely related to Arthrobacter cupressi DSM 24664^T (98.1 % similarity). Average nucleotide identity values between NEAU-SA1^T and A. cupressi DSM 24664^T were 88.91 and 87.41 % by ANIm and ANIb analysis, respectively. The in silico DNA-DNA hybridization value between strain NEAU-SA1^T and A. cupressi DSM 24664^T was 34.20 %, again indicating they belong to different taxa. The genomic DNA G+C content was 66.74 mol%. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The predominant menaquinone was MK-9(H2). The peptidoglycan type was A3α with an interpeptide bridge comprising l-Lys and l-Ala. Glucose, ribose and galactose were the whole-cell sugars. On the basis of morphological, physiological, biochemical and chemotaxonomic analysis, strain NEAU-SA1^T was classified as representing a novel species in the genus Arthrobacter, for which the name Arthrobacter silvisoli sp. nov. is proposed. The type strain is NEAU-SA1^T (=DSM 106716^T=CCTCC AB 2017271^T).

Psychrobacillus lasiicapitis sp. nov., isolated from the head of an ant (Lasius fuliginosus)

A novel Gram-stain-positive, motile, endospore-forming, rod-shaped bacterium, designated strain NEAU-3TGS17^T, was isolated from the head of an ant (Lasius fuliginosus). The isolate grew at 0-35 °C (optimum 28-30 °C), at pH 6.0-11.0 (optimum pH 7.0-8.0) and with 0-6 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-3TGS17^T belonged to the genus Psychrobacillus. Sequence similarities between strain NEAU-3TGS17^T and members of the genus Psychrobacillus with validly published names (Psychrobacillus psychrotolerans DSM 11706^T, Psychrobacillus insolitus DSM 5^T, Psychrobacillus psychrodurans DSM 11713^T and Psychrobacillus soli NBRC 110600^T) were 98.4-99.1 %. DNA-DNA relatedness values between strain NEAU-3TGS17^T and its closest relatives were below 70 %. The major cellular fatty acids (>5 %) were iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and iso-C15 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell-wall peptidoglycan type was A4β with ornithine as the diamino acid and the predominant menaquinones were MK-8 and some MK-7. The DNA G+C content was 35.8 mol%. On the basis of phenotypic data and phylogenetic inference, strain NEAU-3TGS17^T was classified as representing a novel species in the genus Psychrobacillus, for which the name Psychrobacillus lasiicapitis sp. nov. is proposed. The type strain is NEAU-3TGS17^T (=DSM 100484^T=CGMCC 1.15308^T).

Actinobacterial-mediated synthesis of silver nanoparticles and their activity against pathogenic bacteria

In this study, silver nanoparticles (AgNPs) were biosynthesised by using acidophilic actinobacterial SH11 strain isolated from pine forest soil. Isolate SH11 was identified based on 16S rRNA gene sequence to Streptomyces kasugaensis M338-M1^T and S. celluloflavus NRRL B-2493^T (99.8% similarity, both). Biosynthesised AgNPs were analysed by UV-visible spectroscopy, which revealed specific peak at λ = 420 nm. Transmission electron microscopy analyses showed polydispersed, spherical nanoparticles with a mean size of 13.2 nm, while Fourier transform infrared spectroscopy confirmed the presence of proteins as the capping agents over the surface of AgNPs. The zeta potential was found to be -16.6 mV, which indicated stability of AgNPs. The antibacterial activity of AgNPs from SH11 strain against gram-positive (Staphylococcus aureus and Bacillus subtilis) and gram-negative (Escherichia coli) bacteria was estimated using disc diffusion, minimum inhibitory concentration and live/dead analyses. The AgNPs showed the maximum antimicrobial activity against E. coli, followed by B. subtilis and S. aureus. Further, the synergistic effect of AgNPs in combination with commercial antibiotics (kanamycin, ampicillin, tetracycline) was also evaluated against bacterial isolates. The antimicrobial efficacy of antibiotics was found to be enhanced in the presence of AgNPs.