Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum

Streptomyces cynarae sp. nov., a novel actinomycete isolated from the leaves of Cynara scolymus L

Strain HUAS 13-4T, a novel endophytic actinobacterium, was isolated from the leaves of Cynara scolymus L. collected from Changde City in China and characterized using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain HUAS 13-4T shared the highest sequence similarities to Streptomyces leeuwenhoekii C34T (98.90%), Streptomyces harenosi PRKS01-65T (98.83%) and Streptomyces glomeratus LMG 19903T (98.76%). Phylogenetic analysis of 16S rRNA gene sequence indicated that strain HUAS 13-4T was clustered together with Streptomyces bluensis ISP 5564T and Streptomyces cavernae SYSU K10008T. Phylogenomic analysis revealed that strain HUAS 13-4T was most closely related to S. glomeratus JCM 9091T. However, the average nucleotide identity and the digital DNA-DNA hybridization values between them were less than 96.7% and 70% cut-off points recommended for delineating species. Based on a comprehensive comparison of the genome sequences and phenotypic characteristics between strain HUAS 13-4T and its relative, strain HUAS 13-4T (= MCCC 1K08364T = JCM 35919T) should evidently represent a novel Streptomyces species, and the name Streptomyces cynarae sp. nov. is proposed.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

INTRODUCTION

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

METHODS

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

RESULTS

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

DISCUSSION

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Bioprospecting of the novel isolate Microbacterium proteolyticum LA2(R) from the rhizosphere of Rauwolfia serpentina

The study aimed to assess the proficiency of secondary metabolites (SMs) synthesized by actinobacteria isolated from the rhizospheric soil of Rauwolfia serpentina for its antimicrobial and anti-biofilm activity. After morphological and biochemical identification of actinobacteria, primary and secondary screening was done for specific metabolite production. The secondary metabolites were then tested for their antioxidant, antibacterial, and antibiofilm potential. Out of 29 bacterial colonies isolated, only one emerged as a novel isolate, Microbacterium LA2(R). Partial 16S rRNA gene sequence of the isolate LA2(R) was deposited in NCBI GenBank with accession number MN560041. The highest antioxidant capacity of the methanolic extract the novel isolate was found to be 474.183 µL AAE/mL and 319.037 µL AAE/mL by DPPH assay and ABTS assay respectively; three folds higher than the control. These results were further supported by the high total phenolic (194.95 gallic acid equivalents/mL) and flavonoid contents (332.79 µL quercetin equivalents/mL) of the methanolic extract. GC–MS analysis revealed the abundance of antibacterial compounds; where, n-Hexadecanoic acid was found to be the major compound present with a peak of 14 min retention time (RT) and 95% similarity index. MIC value of the metabolite was noted to be around 132.28 ± 84.48 μg/mL. The IC₅₀ value was found to be 74.37, 71.33, 66.28 and 84.48 μg/mL against Escherichia coli, Staphylococcus aureus, Klebsiella pneumonia, and Salmonella abony, respectively. Treatment with IC₅₀ of the extract decreased the biofilm formation up to 70%–80% against pathogenic strains viz. Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae and Salmonella abony. These significant activities of Microbacterium sp. LA2(R) suggests that it could be utilized for antibiotic production for human welfare and in various important industrial applications.

Improving Effects of Afforestation with Different Forest Types on Soil Nutrients and Bacterial Community in Barren Hills of North China

Afforestation can improve soil nutrient content and microbial community structure, increase soil carbon sequestration, and reduce greenhouse gas emissions. However, at present, there is a lack of research on the low hills and mountainous areas in North China. In order to scientifically evaluate the effect of afforestation recovery with different forest types on the improvement of the soil ecological system, the Fanggan ecological restoration in North China was taken as the research sample, and the coniferous forests, mixed coniferous and broad-leaved forest quadrats and broad-leaved forests, as well as the contrast of barren hills bushes were set to achieve the research goals. Research results of different forest types on soil nutrient and bacterial community in the Fanggan ecological restoration area have shown that afforestation with broad-leaved forests most obviously improved the nutrition properties and bacterial community of soil. (1) Broad-leaved forest afforestation obviously improved water retention and ammonia nitrogen content but reduced the content of available phosphorus and nitrate nitrogen of surface soil. It also increased available phosphorus, ammonia nitrogen, and nitrate nitrogen content of lower soil. (2) Broad-leaved forest afforestation significantly increased α-diversity of the bacterial community in surface soil, but only enhanced the Chao1 and ACE indices of lower soil. In addition, afforestation has also significantly changed the structure of soil bacterial community and β-diversity index. (3) Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia accounted for the highest proportion of soil bacterial community. Proteobacteria and Verrucomicrobia occupied higher proportion in broad-leaved forests than in other forest types, while the proportion of Acidobacteria and Actinobacteria was the opposite. (4) Afforestation decreased cooperation and increased competition among bacteria of surface soil as well as increased coexistence and rejection among subsoil bacteria. (5) pH, ammonia nitrogen, organic carbon, and available phosphorus have exhibited a significant impact on the structure of bacterial community in the surface soil, while the bacterial community structure of the lower soil was mainly affected by pH and available phosphorus. Results have fully demonstrated the positive effects of broad-leaved forest on the restoration of soil nutrients and microbial community structure. Meanwhile, the important combinations of soil physical and chemical factors affecting soil bacterial community structure were also explored. The results can provide scientific basis for revealing the mechanism of soil organic matter, nutrient and ecological function restoration by artificial afforestation, and also offer theoretical support and practical reference for the restoration of artificial afforestation in the hilly and mountainous areas of North China.

Ecology and potential functions of plant-associated microbial communities in cold environments

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.

Phylogenetic affiliation of endophytic actinobacteria associated with selected orchid species and their role in growth promotion and suppression of phytopathogens

Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we investigated the culturable endophytic actinobacteria associated with ten epiphytic orchid species of Assam, India. 51 morphologically distinct actinobacteria were recovered from surface sterilized roots and leaves of orchids and characterized based on different PGP and antifungal traits. According to the 16S rRNA gene sequence, these isolates were divided into six families and eight genera, where Streptomyces was most abundant (n=29, 56.86%), followed by Actinomadura, Nocardia, Nocardiopsis, Nocardioides, Pseudonocardia, Microbacterium, and Mycolicibacterium. Regarding PGP characteristics, 25 (49.01%) isolates demonstrated phosphate solubilization in the range of 61.1±4.4 - 289.7±11.9 µg/ml, whereas 27 (52.94%) isolates biosynthesized IAA in the range of 4.0 ± 0.08 - 43.8 ± 0.2 µg/ml, and 35 (68.62%) isolates generated ammonia in the range of 0.9 ± 0.1 - 5.9 ± 0.2 µmol/ml. These isolates also produced extracellular enzymes, viz. protease (43.13%), cellulase (23.52%), pectinase (21.56%), ACC deaminase (27.45%), and chitinase (37.25%). Out of 51 isolates, 27 (52.94%) showed antagonism against at least one test phytopathogen. In molecular screening, most isolates with antifungal and chitinase producing traits revealed the presence of 18 family chitinase genes. Two actinobacterial endophytes, Streptomyces sp. VCLA3 and Streptomyces sp. RVRA7 were ranked as the best strains based on PGP and antifungal activity on bonitur scale. GC-MS examination of ethyl acetate extract of these potent strains displayed antimicrobial compound phenol, 2,4-bis-(1,1-dimethylethyl) as the major metabolite along with other antifungal and plant growth beneficial bioactive chemicals. SEM analysis of fungal pathogen F. oxysporum (MTCC 4633) affected by Streptomyces sp. VCLA3 revealed significant destruction in the spore structure. An in vivo plant growth promotion experiment with VCLA3 and RVRA7 on chili plants exhibited statistically significant (p<0.05) improvements in all of the evaluated vegetative parameters compared to the control. Our research thus gives insight into the diversity, composition, and functional significance of endophytic actinobacteria associated with orchids. This research demonstrates that isolates with multiple plant development and broad-spectrum antifungal properties are beneficial for plant growth. They may provide a viable alternative to chemical fertilizers and pesticides and a sustainable solution for chemical inputs in agriculture.

Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

Coupling of the engineered DNA "mutator" to a biosensor as a new paradigm for activation of silent biosynthetic gene clusters in Streptomyces

DNA replication fidelity in Streptomyces bacteria, prolific producers of many medically important secondary metabolites, is understudied, while in Escherichia coli it is controlled by DnaQ, the ϵ subunit of DNA polymerase III (DNA PolIII). Manipulation of dnaQ paralogues in Streptomyces lividans TK24, did not lead to increased spontaneous mutagenesis in this bacterium suggesting that S. lividans DNA PolIII uses an alternative exonuclease activity for proofreading. In Mycobacterium tuberculosis, such activity is attributed to the DnaE protein representing α subunit of DNA PolIII. Eight DnaE mutants designed based on the literature data were overexpressed in S. lividans, and recombinant strains overexpressing two of these mutants displayed markedly increased frequency of spontaneous mutagenesis (up to 1000-fold higher compared to the control). One of these ‘mutators’ was combined in S. lividans with a biosensor specific for antibiotic coelimycin, which biosynthetic gene cluster is present but not expressed in this strain. Colonies giving a positive biosensor signal appeared at a frequency of ca 10^–5, and all of them were found to produce coelimycin congeners. This result confirmed that our approach can be applied for chemical- and radiation-free mutagenesis in Streptomyces leading to activation of orphan biosynthetic gene clusters and discovery of novel bioactive secondary metabolites.

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.

Phylogenetic and Physiological Diversity of Cultivable Actinomycetes Isolated From Alpine Habitats on the Qinghai-Tibetan Plateau

Actinomycetes in extreme alpine habitat have attracted much attention due to their unique physiological activities and functions. However, little is known about their ecological distribution and diversity. Here, we explored the phylogenetic relationship and physiological heterogeneity of cultivable actinomycetes from near-root soils of different plant communities in the Laohu Ditch (2200 - 4200 m) and Gaize County area (5018 - 5130 m) on the Qinghai-Tibetan Plateau. A total of 128 actinomycete isolates were obtained, 16S rDNA-sequenced and examined for antimicrobial activities and organic acid, H₂S, diffusible pigments, various extracellular enzymes production. Seventy three isolates of the total seventy eight isolates from the Laohu Ditch, frequently isolated from 2200 to 4200 m, were closely related to Streptomyces spp. according to the 16S rDNA sequencing, while four isolates within the genus Nocardia spp. were found at 2200, 2800, and 3800 m. In addition, one potential novel isolate with 92% sequence similarity to its nearest match Micromonospora saelicesensis from the GenBank database, was obtained at 2200 m. From the Gaize County area, fifty Streptomyces isolates varied in diversity at different sites from 5018 to 5130 m. The investigation of phenotypic properties of 128 isolates showed that 94.5, 78.9, 68, 64.8, 53, 51.6, 50, 36.7, 31.2, and 22.7% of the total isolates produced catalase, lipase 2, urease, protease, H₂S, lipase 3, amylase, lipase 1, diffusible pigment and organic acid, respectively. The antimicrobial assays of the total isolates revealed that 5, 28, 19, and 2 isolates from Streptomyces spp. exhibited antimicrobial activity against Escherichia coli, Staphylococcus aureus, Candida albicans, and Pseudomonas aeruginosa, respectively. This study intends to bring helpful insights in the exploitation and utilization of alpine actinomycetes for novel bioactive compounds discovery.

Viennamycins: Lipopeptides Produced by a Streptomyces sp

Extracts from Streptomyces sp. S4.7 isolated from the rhizosphere of edelweiss, an alpine medicinal plant, exhibited activity against Gram-positive bacteria. LC-HRMS analyses of the extracts resulted in the detection of two unknown, structurally related lipopeptides that were assumed to be responsible for the antibiotic activity. LC-MS guided isolation and structure elucidation of viennamycins A and B (1 and 2) by HR-MS/MS, 1D and 2D NMR, and Marfey's analyses revealed them to be novel compounds, with viennamycin A containing cysteic acid, a unique feature for lipopeptides. Tests for antibacterial, antifungal, and cytotoxic activities of purified viennamycins, both with and without divalent cations, did not reveal any bioactivity, suggesting that their biological function, which could not be determined in the tests used, is atypical for lipopeptides. The genome of Streptomyces sp. S4.7 was sequenced and analyzed, revealing the viennamycin biosynthetic gene cluster. Detailed bioinformatics-based analysis of the viennamycin gene cluster allowed elucidation of the biosynthetic pathway for these lipopeptides.

Streptomyces from traditional medicine: sources of new innovations in antibiotic discovery

Given the increased reporting of multi-resistant bacteria and the shortage of newly approved medicines, researchers have been looking towards extreme and unusual environments as a new source of antibiotics. Streptomyces currently provides many of the world's clinical antibiotics, so it comes as no surprise that these bacteria have recently been isolated from traditional medicine. Given the wide array of traditional medicines, it is hoped that these discoveries can provide the much sought after core structure diversity that will be required of a new generation of antibiotics. This review discusses the contribution of Streptomyces to antibiotics and the potential of newly discovered species in traditional medicine. We also explore how knowledge of traditional medicines can aid current initiatives in sourcing new and chemically diverse antibiotics.

Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments

A novel marine actinobacterium, strain SCSIO 58843^T, was isolated from the sediment sample collected from the South China Sea. Strain SCSIO 58843^T was Gram-stain-positive, aerobic and rod shaped. The whole-cell hydrolysis of amino acids contained dd-DAP, alanine, glutamic acid, glycine and aspartic acid. The main menaquinone was MK-9(H₈). The major fatty acids were C_17 : 1  ω8c and C_17 : 0. The major phospholipids were diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phospatidylcholine (PC) and phosphatidylinositolmannoside (PIM). The G+C content of the genomic DNA was 72.5 %. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 58843^T formed a new lineage in the family Iamiaceae and had the highest similarity of 93.8 % with Iamia majanohamensis DSM 19957^T. Strain SCSIO 58843^T can be distinguished from these known genera in the family Iamiaceae by polyphasic data analyses, and represents a novel genus and novel species, for which Actinomarinicola tropica gen. nov., sp. nov is proposed with the type strain SCSIO 58843^T(=KCTC 49408^T=CGMCC 1.17503^T).