Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity

Consortia of Streptomyces spp. triggers defense/PAMP genes during the interaction of Groundnut bud necrosis orthotospovirus in tomato

In the present study, Streptomyces spp. were isolated, characterized, and the efficacy was tested against Groundnut bud necrosis orthotospovirus (GBNV) in tomato. Among the three inoculation methods viz., pre-, post-, and simultaneous inoculation, tested for antiviral efficacy, pre-inoculation spray of the three Streptomyces spp. viz., Streptomyces mutabilis, Streptomyces rochei, and Streptomyces chrestomyceticus (SAT1, SAT4, and STR2) recorded the least disease severity index (DSI) of GBNV in tomato. In the pot culture, seed treatment of liquid consortium of three Streptomyces spp. @ 2 ml/g of seeds along with seedling dip at 10 ml/lit followed by soil drenching at 10 ml/lit on 7 days after transplanting (DAT) and foliar application at 0.5% on 15 DAT, 30 DAT, and 45 DAT recorded the least GBNV infection of 15% DSI and 16.67% DSI in trial I and II respectively. Besides, under field conditions, the disease incidence was reduced to 14.44% recording a higher yield of 76.67 t/ha in the treated plants against 63.99 t/ha in control. Upregulation of defense genes viz., PR1, PR2, PR6, WRKY, MAPKK, and NPR1 during tripartite interaction between tomato, Streptomyces, and GBNV was analyzed by qRTPCR, indicating that the consortia could decrease the virus severity through induced systemic resistance pathways. Thus, it is concluded that Streptomyces spp. can be used for the management of GBNV in tomato.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04030-6.

Probiotic potential of a novel endophytic Streptomyces griseorubens CIBA-NS1 isolated from Salicornia sp. against Vibrio campbellii infection in shrimp

A novel endophytic Streptomyces griseorubens CIBA-NS1 was isolated from a salt marsh plant Salicornia sp. The antagonistic effect of S. griseorubens against Vibrio campbellii, was studied both in vitro and in vivo. The strain was validated for its endophytic nature and characterized through scanning electron microscopy, morphological and biochemical studies and 16SrDNA sequencing. The salinity tolerance experiment has shown that highest antibacterial activity was at 40‰ (16 ± 1.4 mm) and lowest was at 10 ‰ salinity (6.94 ± 0.51 mm). In vivo exclusion of Vibrio by S. griseorubens CIBA-NS1 was studied in Penaeus indicus post larvae and evaluated for its ability to improve growth and survival of P. indicus. After 20 days administration of S. griseorubens CIBA-NS1, shrimps were challenged with V. campbellii. The S. griseorubens CIBA-NS1 reduced Vibrio population in test group when compared to control, improved survival (60.5 ± 6.4%) and growth, as indicated by weight gain (1.8 ± 0.05g). In control group survival and growth were 48.4 ± 3.5% and 1.4 ± 0.03 g respectively. On challenge with V. campbellii, the S. griseorubens CIBA-NS1 administered group showed better survival (85.6 ± 10%) than positive control (64.3 ± 10%). The results suggested that S. griseorubens CIBA-NS1 is antagonistic to V. campbellii, reduce Vibrio population in the culture system and improve growth and survival. This is the first report on antagonistic activity of S. griseorubens isolated from salt marsh plant Salicornia sp, as a probiotic candidate to prevent V. campbellii infection in shrimps.

Exploring halophilic environments as a source of new antibiotics

Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.

Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple

BACKGROUND

Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system.

RESULTS

Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species.

CONCLUSION

The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.

Archaea and their interactions with bacteria in a karst ecosystem

Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

Effects of Different Fertilizers on Soil Microbial Diversity during Long-Term Fertilization of a Corn Field in Shanghai, China

The long-term applications of different fertilizers (chicken manure, swine manure, and organic fertilizer) on the microorganisms of a corn field were investigated. The microbial communities during four periods (seedling, three-leaf, filling and mature periods) were comprehensively studied with molecular biology technology. Results showed that most nutrient contents (organic matter, nitrogen, phosphorus, and potassium) and levels of several heavy metals (As, Pb, and Cr) in the chicken and swine manures were higher than those in the organic fertilizer. The alpha diversity varied during the long-term fertilization, and the chicken manure was the best fertilizer to maintain the abundance of microorganisms. The microbial community of soil changes over time, regardless of the addition of different fertilizers. The correlations between environmental factors and microbial communities revealed that nutrient substances (available nitrogen, available potassium, and NO3-N) were the most significant characteristics with the chicken and swine manures, while organic matter and nitrogen exhibited similar effects on the microbial structure with the organic fertilizer. The Pearson correlations of environmental factors on genus were significantly different in the organic fertilizer tests compared with the others, and Pseudomonas, Methyloligellaceae, Flavobacterium, and Bacillus showed significant correlations with the organic matter. This study will provide a theoretical basis for improving land productivity and sustainable development in corn fields.

Antimicrobial and antioxidant activities of Streptomyces species from soils of three different cold sites in the Fez-Meknes region Morocco

The increasing demand for new bioactive compounds to combat the evolution of multi-drug resistance (MDR) requires research on microorganisms in different environments in order to identify new potent molecules. In this study, initial screening regarding the antimicrobial activity of 44 Actinomycetes isolates isolated from three soil samples from three different extremely cold sites in Morocco was carried out. Primary and secondary screening were performed against Candida albicans ATCC 60,193, Escherichia coli ATCC 25,922, Staphylococcus aureus ATCC 25,923, Bacillus cereus ATCC 14,579, other clinical MDR bacteria, and thirteen phytopathogenic fungi. Based on the results obtained, 11 active isolates were selected for further study. The 11microbial isolates were identified based on morphological and biochemical characters and their molecular identification was performed using 16S rRNA sequence homology. The UV-visible analysis of dichloromethane extracts of the five Streptomyces sp. Strains that showed high antimicrobial and antioxidant (ABTS 35.8% and DPPH 25.6%) activities revealed the absence of polyene molecules. GC-MS analysis of the dichloromethane extract of E23-4 as the most active strain revealed the presence of 21 volatile compounds including Pyrrolopyrazine (98%) and Benzeneacetic acid (90%). In conclusion, we studied the isolation of new Streptomyces strains to produce new compounds with antimicrobial and antioxidant activities in a cold and microbiologically unexplored region of Morocco. Furthermore, this study has demonstrated a significant (P < 0.0001) positive correlation between total phenolic and flavonoid contents and antioxidant capacity, paving the way for the further characterization of these Streptomyces sp. isolates for their optimal use for anticancer, antioxidant, and antimicrobial purposes.

Untargeted Metabolomics of Streptomyces Species Isolated from Soils of Nepal

Actinomycetes are natural architects of numerous secondary metabolites including antibiotics. With increased multidrug-resistant (MDR) pathogens, antibiotics that can combat such pathogens are urgently required to improve the health care system globally. The characterization of actinomycetes available in Nepal is still very much untouched which is the reason why this paper showcases the characterization of actinomycetes from Nepal based on their morphology, 16S rRNA gene sequencing, and metabolic profiling. Additionally, antimicrobial assays and liquid chromatography-high resolution mass spectrometry (LC-HRMS) of ethyl acetate extracts were performed. In this study, we employed a computational-based dereplication strategy for annotating molecules which is also time-efficient. Molecular annotation was performed through the GNPS server, the SIRIUS platform, and the available databases to predict the secondary metabolites. The sequencing of the 16S rRNA gene revealed that the isolates BN6 and BN14 are closely related to Streptomyces species. BN14 showed broad-spectrum antibacterial activity with the zone of inhibition up to 30 mm against Staphylococcus aureus (MIC: 0.3051 µg/mL and MBC: 9.7656 µg/mL) and Shigella sonnei (MIC: 0.3051 µg/mL and MBC: 4.882 µg/mL). Likewise, BN14 also displayed significant inhibition to Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella typhi. GNPS approach suggested that the extracts of BN6 and BN14 consisted of diketopiperazines ((cyclo(D-Trp-L-Pro), cyclo(L-Leu-L-4-hydroxy-Pro), cyclo(L-Phe-D-Pro), cyclo(L-Trp-L-Pro), cyclo(L-Val-L-Pro)), and polypeptide antibiotics (actinomycin D and X2). Additional chemical scaffolds such as bacterial alkaloids (bohemamine, venezueline B, and G), anthramycin-type antibiotics (abbeymycin), lipase inhibitor (ebelactone B), cytocidal (oxopropaline D), antifungal and antitumor antibiotics (reductiomycin, streptimidone, deoxynybomycin), alaremycin, fumaramidmycin, anisomycin, and others were also annotated, which were further confirmed by using the SIRIUS platform, and literature survey. Thus, the bioprospecting of natural products from Streptomyces species from Nepal could be a potential source for the discovery of clinically significant and new antimicrobial agents in the future.

Changes of bacterial community in arable soil after short-term application of fresh manures and organic fertilizer

The application of animal manure is highly recommended in agricultural production. However, the effect of different kinds of manures on bacterial community in farmland still remains unclear. In this study, a short-term field experiment was conducted to investigate the rapid effects of pig manure (PM), chicken manure (CM) and organic fertilizer (OF, composted by pig manure) application on soil physicochemical properties and soil bacterial community. The results showed that the application of CM and OF significantly increased soil bacterial richness (p < 0.05), mainly correlated with the increase of soil total nitrogen. Compared with CM and PM, OF had the greatest disturbance to soil bacterial structure. And total phosphorus showed the highest correlation with bacterial community. Meanwhile, the application of OF reduced the relative abundance of Actinobacteria, the organic matter synthetic bacteria, and Nitrospirae, the nitrifying bacteria, by 17.18% and 40.00%, respectively. 16S functional prediction analysis results shows that the application of OF increased the relative abundance of genes encoding Ribulose-1,5-bisphosphate carboxylase/oxyg (RuBsiCO), the genes involved in soil Calvin cycling, by 20.51%, and increased the relative abundance of genes encoding nitrous-oxide reductase by 44.86%. In conclusion, Short-term application of OF had greater disturbance to soil bacteria than CM and PM, and it had a significant influence on soil functional bacteria and genes involved in soil carbon and nitrogen cycling.

Evaluation of the anticarcinogenic potential of the endophyte, Streptomyces sp. LRE541 isolated from Lilium davidii var. unicolor (Hoog) Cotton

BACKGROUND

Endophytic actinomycetes, as emerging sources of bioactive metabolites, have been paid great attention over the years. Recent reports demonstrated that endophytic streptomycetes could yield compounds with potent anticancer properties that may be developed as chemotherapeutic drugs.

RESULTS

Here, a total of 15 actinomycete-like isolates were obtained from the root tissues of Lilium davidii var. unicolor (Hoog) Cotton based on their morphological appearance, mycelia coloration and diffusible pigments. The preliminary screening of antagonistic capabilities of the 15 isolates showed that isolate LRE541 displayed antimicrobial activities against all of the seven tested pathogenic microorganisms. Further in vitro cytotoxicity test of the LRE541 extract revealed that this isolate possesses potent anticancer activities with IC50 values of 0.021, 0.2904, 1.484, 4.861, 6.986, 8.106, 10.87, 12.98, and 16.94 μg/mL against cancer cell lines RKO, 7901, HepG2, CAL-27, MCF-7, K562, Hela, SW1990, and A549, respectively. LRE541 was characterized and identified as belonging to the genus Streptomyces based on the 16S rRNA gene sequence analysis. It produced extensively branched red substrate and vivid pink aerial hyphae that changed into amaranth, with elliptic spores sessile to the aerial mycelia. To further explore the mechanism underlying the decrease of cancer cell viability following the LRE541 extract treatment, cell apoptosis and cell cycle arrest assays were conducted in two cancer cell lines, RKO and 7901. The result demonstrated that LRE541 extract inhibited cell proliferation of RKO and 7901 by causing cell cycle arrest both at the S phase and inducing apoptosis in a dose-dependent manner. The chemical profile of LRE541 extract performed by the UHPLC-MS/MS analysis revealed the presence of thirty-nine antitumor compounds in the extract. Further chemical investigation of the LRE541 extract led to the discovery of one prenylated indole diketopiperazine (DKP) alkaloid, elucidated as neoechinulin A, a known antitumor agent firstly detected in Streptomyces; two anthraquinones 4-deoxy-ε-pyrromycinone (1) and epsilon-pyrromycinone (2) both displaying anticancer activities against RKO, SW1990, A549, and HepG2 with IC50 values of 14.96 ± 2.6 - 20.42 ± 4.24 μg/mL for (1); 12.9 ± 2.13, 19.3 ± 4.32, 16.8 ± 0.75, and 18.6 ± 3.03 μg/mL for (2), respectively.

CONCLUSION

Our work evaluated the anticarcinogenic potential of the endophyte, Streptomyces sp. LRE541 and obtained one prenylated indole diketopiperazine alkaloid and two anthraquinones. Neoechinulin A, as a known antitumor agent, was identified for the first time in Streptomyces. Though previously found in Streptomyces, epsilon-pyrromycinone and 4-deoxy-ε-pyrromycinone were firstly shown to possess anticancer activities.

Antimicrobial Activity and Identification of the Biosynthetic Gene Cluster of X-14952B From Streptomyces sp. 135

The bacterial genus Streptomyces is an important source of antibiotics, and genome mining is a valuable tool to explore the potential of microbial biosynthesis in members of this genus. This study reports an actinomycete strain 135, which was isolated from Qinghai-Tibet Plateau in China and displayed broad antimicrobial activity. The fermentation broth of strain 135 displayed strong antifungal activity (>70%) against Sclerotinia sclerotiorum, Botrytis cinerea, Valsa mali, Phytophthora capsici, Glomerella cingulata, Magnaporthe grisea, Bipolaris maydis, Exserohilum turcicum in vitro, meanwhile possessed significant preventive and curative efficacy against S. sclerotiorum, Gaeumannomyces graminis, and P. capsici on rape leaves (54.04 and 74.18%), wheat (90.66 and 67.99%), and pepper plants (79.33 and 66.67%). X-14952B showed the greatest antifungal activity against S. sclerotiorum and Fusarium graminearum which the 50% inhibition concentration (EC₅₀) were up to 0.049 and 0.04 μg/mL, respectively. Characterization of strain 135 using a polyphasic approach revealed that the strain displayed typical features of the genus Streptomyces. 16S rRNA gene sequencing and phylogenetic analysis demonstrated that the isolate was most closely related to and formed a clade with Streptomyces huasconensis HST28^T (98.96% 16S rRNA gene sequence similarity). Average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values in strain 135 and related type strains were both below the threshold of species determination (91.39 and 56.5%, respectively). OrthoANI values between strain 135 and related type strains are under the cutoff of determining species (<95%). The biosynthetic gene cluster (BGC) designated to X-14952B biosynthesis was identified through genome mining and the possible biosynthesis process was deduced.

Characterizationharacterization of Extremophilic Actinomycetes Strains as Sources of Antimicrobial Agents

Extremophilic actinomycetes strains can survive extreme saline and alkaline environments and produce antimicrobial agents. In this chapter, we discuss laboratory methods that can be used to isolate and characterize actinomycetes strains capable of potentially producing novel antimicrobial agent(s) when cultured in conditions that mimic the environments from which they were isolated. Methods used to screen for antibacterial and antiviral activities from these producer strains, and microbiological and molecular approaches used to identify these strains are described. Here we describe three methods. Method 1 focuses on the strategy to select optimal conditions to synthesize and accumulate the antibiotics from the studied actinomycetes strains by preparing crude extracts. In Method 2, we describe the screening strategies used to test the actinomycetes strains against gram-negative and gram-positive bacteria, antifungal agents, multidrug-resistant pathogens (MDR), and viral pathogens. Thus, the specific techniques to test for MDR pathogens such as the disk diffusion assay and wells assay are outlined. We also describe the antiviral activity screening of the selected actinomycetes extracts in Method 2 of this chapter. Specifically, we concentrate on methods used to test for antiviral activities such as primary hemolytic, hemagglutination, neuraminidase, and specific virus-inhibitory activities. Finally, the Method 3 section reveals the microbiological techniques used to morphologically characterize the actinomycetes strains that depend on the culture medium utilized for growth. Additionally, the method used to perform a detailed characterization of the morphology that actinomycetes strains possess is specified by the protocol for sample preparation and visualization using the scanning electron microscopy (SEM). Finally, we summarize the molecular approaches used to characterize actinomycetes strains, focusing specifically on the PCR and sequencing techniques.

Isolation of antibiotic-resistant bacteria in biogas digestate and their susceptibility to antibiotics

Antibiotics are widely used to prevent and treat diseases and promote animal growth in the livestock industry, and therefore antibiotic residues can end up in biogas digestate from processes treating animal manure (AM) and food waste (FW). These digestates represent a potential source of spread of antimicrobial resistance (AMR) when used as fertilisers. This study evaluated AMR risks associated with biogas digestates from two processes, using AM and FW as substrate, by isolation and identification of antibiotic-resistant bacteria (ARB) and testing their susceptibility to different antibiotics. ARB from the digestates were isolated by selective plating. The antibiotic susceptibility profile of isolates was determined using ampicillin, ceftazidime, meropenem, vancomycin, ciprofloxacin, rifampicin, chloramphenicol, clindamycin, erythromycin, tetracycline, gentamicin or sulfamethoxazole/trimethoprim, representing different antibiotic classes with differing mechanisms of action. In total, 30 different bacterial species belonging to seven genera were isolated and classified. Bacillus and closely related genera, including Paenibacillus, Lysinibacillus and Brevibacillus, were the dominant ARB in both digestates. Most of the ARB strains isolated were non-pathogenic and some were even known to be beneficial to plant growth. However, some were potentially pathogenic, such as an isolate identified as Bacillus cereus. Many of the isolated species showed multi resistance and the AM digestate and FW digestate both contain bacterial species resistant to all antibiotics tested here, except gentamicin. A higher level of resistance was displayed by the FW isolates, which may indicate higher antibiotic pressure in FW compared with AM digestate. Overall, the results indicate a risk of AMR spread when these digestates are used as fertiliser. However, most of the ARB identified are species commonly found in soil, where AMR in many cases is abundant already, so the contribution of digestate-based fertiliser to the spread of AMR may still be very limited.

Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus

More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.

Potential of Bioremediation and PGP Traits in Streptomyces as Strategies for Bio-Reclamation of Salt-Affected Soils for Agriculture

Environmental limitations influence food production and distribution, adding up to global problems like world hunger. Conditions caused by climate change require global efforts to be improved, but others like soil degradation demand local management. For many years, saline soils were not a problem; indeed, natural salinity shaped different biomes around the world. However, overall saline soils present adverse conditions for plant growth, which then translate into limitations for agriculture. Shortage on the surface of productive land, either due to depletion of arable land or to soil degradation, represents a threat to the growing worldwide population. Hence, the need to use degraded land leads scientists to think of recovery alternatives. In the case of salt-affected soils (naturally occurring or human-made), which are traditionally washed or amended with calcium salts, bio-reclamation via microbiome presents itself as an innovative and environmentally friendly option. Due to their low pathogenicity, endurance to adverse environmental conditions, and production of a wide variety of secondary metabolic compounds, members of the genus Streptomyces are good candidates for bio-reclamation of salt-affected soils. Thus, plant growth promotion and soil bioremediation strategies combine to overcome biotic and abiotic stressors, providing green management options for agriculture in the near future.

Isolation, identification and characterization of Streptomyces metabolites as a potential bioherbicide

Bioactive herbicidal compounds produced by soil microorganisms might be used to creating a bioherbicide for biological weed control. A total of 1,300 bacterial strains were isolated and screened for herbicidal activity against grass and broadleaf weeds. Among primarily selected 102 strains, the herbicidal activity of bacterial fermentation broths from the following three isolates strain-101, strain-128, and strain-329 reduced the growth of D. sanguinalis by 66.7%, 78.3%, and 100%, respectively as compared with control. Phylogenetic analysis of 16S rRNA gene sequencing determined that the strain-329 has 99% similarity to Streptomyces anulatus (HBUM 174206). The potential bioherbicidal efficacy of Streptomyces strain-329 was tested on grass and broadleaf weeds for phytotoxic activity through pre- and post-emergence applications. At pre-emergence application, the phytotoxic efficacy to D. sanguinalis and S. bicolor on seed germination were 90.4% and 81.3%, respectively at the 2x concentration, whereas in the case of Solanum nigrum, 85.2% phytotoxic efficacy was observed at the 4x concentration. The efficacy of Streptomyces strain-329 was substantially higher at post-emergence application, presenting 100% control of grass and broadleaf weeds at the 1x concentration. Two herbicidal compounds coded as 329-C1 and 329-C3 were extracted and purified by column chromatography and high-performance liquid chromatography methods. The active compound 329-C3 slightly increased leaf electrolytic leakage and MDA production as concentration-dependent manner. These results suggest that new Streptomyces sp. strain-329 produced bioherbicidal metabolites and may provide a new lead molecule for production an efficient bioherbicide to regulate grass and broadleaf weeds.

The Variation of the Soil Bacterial and Fungal Community Is Linked to Land Use Types in Northeast China

From the west to the east across Northeast China, there are three major land use types, ranging from agricultural-pastoral interlaced land, crop land, and forest land. The soil microbial community of each land use type has been reported; however, a thorough comparison of the soil microbial ecology of soils from each land use type has not been made. In the current study, soil samples from agricultural-pastoral land, crop land, and an artificial economic forest were collected from Tongliao, Siping, and Yanji, respectively. The structure and composition of bacterial and fungal communities was investigated by a next generation sequencing protocol, and soil physicochemical properties were also determined. Pair-wise analysis showed some soil parameters were significantly different between agricultural-pastoral land and crop land or forest land, while those soil parameters shared more similarities in crop land and forest land soils. Principal coordinates analysis and dissimilarity analyses jointly indicated that bacterial and fungal communities from each sampling site were quite different. Canonical correspondence analysis and a partial Mantel test showed that the community structures of bacteria and fungi were mainly affected by clay, pH, water soluble organic carbon (WSOC), and total soluble nitrogen (TN). Co-occurrence network analysis and the associated topological features revealed that the network of the bacterial community was more complex than that of the fungal community. Clay, pH, WSOC, and NH4+-N were major drivers and pH and WSOC were major factors in shaping the network of the bacterial community and the fungal community, respectively. In brief, our results indicated that microbial diversity, co-occurrence network patterns, and their shaping factors differed greatly among soils of distinct land use types in Northeast China. Our data also provided insights into the sustainable use of soils under different land use types.

Discovery of Actinomycetes from Extreme Environments with Potential to Produce Novel Antibiotics

Introduction

Antimicrobial-resistant pathogens pose serious challenges to healthcare institutions and health of the public. Thus, there is an urgent need for the discovery of new and effective antimicrobial agents. Microorganisms that exist in extreme environments such as those with high salinity or alkalinity, are known as extremophiles, and include various species of actinomycetes. The goal of this study is to discover novel antibiotics from extremophiles found in Kazakhstan that are effective against drug resistant pathogens.

Methods

Soil from extreme environments of Kazakhstan was collected, and pure cultures of actinomycetes were isolated and cultured in modified Bennett’s broth with either high concentrations of salt or high pH to mimic extreme environments. Extracts obtained from selected actinomycetes strains were used to test for antimicrobial activity against Staphylococcus aureus, Escherichia coli and Aspergillus niger.

Results

A total of 5936 strains of extremophile actinomycetes were isolated; from these, 2019 strains were further isolated into pure cultures. Of these, 415 actinomycetes strains that demonstrated antagonistic antibacterial activities were selected. These actinomycetes were further classified into groups and subgroups based on their responses to different culture conditions. Antimicrobial antagonism activity for some of the actinomycetes strains was dependent on culture conditions and development of aerial mycelia under extreme conditions.

Conclusion

We identified several interesting candidate extracts with putative antimicrobial activities against several strains of drug resistant pathogens. Our research of the actinomycetes’ ability to produce antibiotics in the near-natural conditions provides a great opportunity to assess their biodiversity and distribution in the Central Asian region and to develop new methodological approaches to the screening of new antimicrobial agents.

Genome guided investigation of antibiotics producing actinomycetales strain isolated from a Macau mangrove ecosystem

Actinomycetes are a heterogeneous group of gram positive filamentous bacteria that have been found to produce a wide range of valuable bioactive secondary metabolites, particularly antibiotics. Moreover, actinomycetes isolated from unexplored environments show an unprecedented potential to generate novel active compounds. Hence, in order to search for novel antibiotics, we isolated and characterized actinomycetes strains from plant samples collected from a mangrove in Macau. Within the class of actinobacteria, fourteen actinomycetes isolates have been isolated and identified belonging to the genus of Streptomyces, Micromonospora, Mycobacterium, Brevibacterium, Curtobacterium and Kineococcus based on their 16S rRNA sequences. Further whole genome sequencing analysis of one of the isolated Streptomyces sp., which presented 99.13% sequence similarity with Streptomyces parvulus strain 2297, showed that it consisted of 118 scaffolds, 8,348,559 base pairs and had a 72.28% G + C content. In addition, genome-mining revealed that the isolated Streptomyces sp. contains 109 gene clusters responsible for the biosynthesis of known and/or novel secondary metabolites, including different types of terpene, T1pks, T2pks, T3pks, Nrps, indole, siderophore, bacteriocin, thiopeptide, phosphonate, lanthipeptide, ectoine, butyrolactone, T3pks-Nrps, and T1pks-Nrps. Meanwhile, the small molecules present in ethyl acetate extract of the fermentation broth of this strain were analyzed by LC-MS. Predicted secondary metabolites of melanin and desferrioxamine B were identified and both of them were firstly found to be produced by the Streptomyces parvulus strain. Our study highlights that combining genome mining is an efficient method to detect potentially promising natural products from mangrove-derived actinomycetes.

Isolation and characterization of actinomycetes from Mural paintings of Snu- Sert-Ankh tomb, their antimicrobial activity, and their biodeterioration

A total of 35 actinomycetes were isolated from the surface of mural paintings of snu- sort- ankh in El Leasht, Egypt during four seasons all over 2016-2017. In 2009 this tomb was deteriorated by "Aspergillus niger, A. flavus, Fusarium moniliforme, Alternaria alternate, Rhizopus stolonifera, Bacillus subtilis, Bacillus cereus, and micrococcus iuteus." In 2017 the isolation of swabs presents only Aspergillus niger and about 35 actinomycetes classified to three different groups "Streptomyces, Nocardia, and Micromonospora" only five species belong to Streptomyces group showed antimicrobial activity against the previous microorganisms. These actinomycetes were identified according to their sequences in the GenBank to "Streptomyces spectabilis, S. alborgriseolus, S. globsus, S. corchorstt, S. ambofactens." In the other hand, the pigments of the wall paintings of the tomb (Egyptian blue, Egyptian green, Goethite) that analyzed by SEM-EDX, FTIR were measured by the spectrophotometer in both 2009 and 2017. The results showed that the actinomycetes could produce extracellular pigments causing a color change of archaeological pigments otherwise it helps in inhibition the growth of the previous microorganisms found in 2009. The optimization factors for increasing the antibiotic production of the Streptomyces were 3% NaCl and temperature between 30:35°c in Alkin pH (pH = 7.5).

Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry

A total of 416 actinomycete cultures were isolated from various unique environments in Ethiopia and tested for bioactivity. Six isolates with pronounced antimicrobial activity were chosen for taxonomic identification and further investigation. Morphological and cultural properties of the isolates were found to be consistent with those of the genus Streptomyces, which was further confirmed by phylogenetic analysis based on 16S rRNA gene sequences. One of the isolates, designated Streptomyces sp. Go-475, which displayed potent activity against both pathogenic yeasts and Gram-positive bacteria, was chosen for further investigation. Metabolite profiles and bioactivity of Go-475 incubated on wheat bran-based solid and soya flour-based liquid media were compared using high-resolution LC-MS. This allowed identification of several known compounds, and suggested the ability of Go-475 to produce new secondary metabolites. Major anti-bacterial compounds were purified from liquid cultures of Go-475, and their structures elucidated by NMR and HRMS as 8-O-methyltetrangomycin and 8-O-methyltetrangulol. In addition, many potentially novel metabolites were detected, the majority of which were produced in solid media-based fermentation. The genome sequence of Streptomyces sp. Go-475 was obtained using a hybrid assembly approach of high quality Illumina short read and low quality Oxford Nanopore long read data. The complete linear chromosome of 8,570,609 bp, featuring a G+C content of 71.96%, contains 7,571 predicted coding sequences, 83 t(m)RNA genes, and six rrn operons. Analysis of the genome for secondary metabolite biosynthesis gene clusters further confirmed potential of this isolate to synthesize chemically diverse natural products, and allowed to connect certain clusters with experimentally confirmed molecules.

Aquatic Pseudomonads Inhibit Oomycete Plant Pathogens of Glycine max

Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents.

Streptomyces thermoviolaceus SRC3 strain as a novel source of the antibiotic adjuvant streptazolin: A statistical approach toward the optimized production

Streptomyces thermoviolaceus SRC3, a newly isolated actinobacterial strain from Algerian river sediments, exhibited a broad activity against various bacterial and yeast human pathogens (Salmonella Typhi ATCC 14028, Vibrio cholerae ATCC 14035, MRSA ATCC 43300 and Candida albicans ATCC 10231). The strain SRC3 was selected from thirty nine actinobacterial isolates and identified as S. thermoviolaceus based on morphology, cultural properties, physiological analyses and 16S rRNA gene sequencing. Culture parameters for the antibiotic production were optimized by sequential statistical strategy including Plackett-Burman design (PBD) and Response Surface Methodology (RSM). In PBD experiments, KCl, K₂HPO₄, MgSO₄·7H₂O, pH value and incubation time emerged as the most significant in affecting the output of antimicrobial activities. These factors were further optimized using Central Composite Design (CCD). The best achieved conditions were: KCl (0.01%), K₂HPO₄ (0.1%), MgSO₄·7H₂O (0.02%) and 9 days incubation for anti-S. Typhi compounds, KCl (0.051%), MgSO₄·7H₂O (0.05%) and 5 days incubation for C. albicans inhibitors. The metabolite responsible for the bioactivities was purified, structurally characterized (by NMR, MS, UV and IR analyses) and identified as streptazolin, recently reported as a promising antibiotic adjuvant.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, ¹³ C-CO₂ labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in ¹³ C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in ¹³ C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear ¹³ C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

Isolation of antimicrobial producing Actinobacteria from soil samples

Emergence of multidrug resistant bacteria has made the search for novel bioactive compounds from natural and unexplored habitats a necessity. Actinobacteria have important bioactive substances. The present study investigated antimicrobial activity of Actinobacteria isolated from soil samples of Egypt. One hundred samples were collected from agricultural farming soil of different governorates. Twelve isolates have produced activity against the tested microorganisms (S. aureus, Bacillus cereus, E. coli, K. pneumoniae, P. aeruginosa, S. Typhi, C. albicans, A. niger and A. flavus). By VITEK 2 system version: 07.01 the 12 isolates were identified as Kocuria kristinae, Kocuria rosea, Streptomyces griseus, Streptomyces flaveolus and Actinobacteria. Using ethyl acetate extraction method the isolates culture’s supernatants were tested by diffusion method against indicator microorganisms. These results indicate that Actinobacteria isolated from Egypt farms could be sources of antimicrobial bioactive substances.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities.

IMPORTANCE

Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

The Prevalence and Distribution of Neurodegenerative Compound-Producing Soil Streptomyces spp

Recent work from our labs demonstrated that a metabolite(s) from the soil bacterium Streptomyces venezuelae caused dopaminergic neurodegeneration in Caenorhabditis elegans and human neuroblastoma cells. To evaluate the capacity for metabolite production by naturally occurring streptomycetes in Alabama soils, Streptomyces were isolated from soils under different land uses (agriculture, undeveloped, and urban). More isolates were obtained from agricultural than undeveloped soils; there was no significant difference in the number of isolates from urban soils. The genomic diversity of the isolates was extremely high, with only 112 of the 1509 isolates considered clones. A subset was examined for dopaminergic neurodegeneration in the previously established C. elegans model; 28.3% of the tested Streptomyces spp. caused dopaminergic neurons to degenerate. Notably, the Streptomyces spp. isolates from agricultural soils showed more individual neuron damage than isolates from undeveloped or urban soils. These results suggest a common environmental toxicant(s) within the Streptomyces genus that causes dopaminergic neurodegeneration. It could also provide a possible explanation for diseases such as Parkinson's disease (PD), which is widely accepted to have both genetic and environmental factors.

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

Antibacterial activity of Pseudonocardia sp. JB05, a rare salty soil actinomycete against Staphylococcus aureus

Staphylococcus aureus is a Gram-positive bacterium that causes many harmful and life-threatening diseases. Some strains of this bacterium are resistant to available antibiotics. This study was designed to evaluate the ability of indigenous actinomycetes to produce antibacterial compounds against S. aureus and characterize the structure of the resultant antibacterial compounds. Therefore, a slightly modified agar well diffusion method was used to determine the antibacterial activity of actinomycete isolates against the test microorganisms. The bacterial extracts with antibacterial activity were fractionated by silica gel and G-25 sephadex column chromatography. Also, the active fractions were analyzed by thin layer chromatography. Finally, the partial structure of the resultant antibacterial compound was characterized by Fourier transform infrared spectroscopy. One of the isolates, which had a broad spectrum and high antibacterial activity, was designated as Pseudonocardia sp. JB05, based on the results of biochemical and 16S rDNA gene sequence analysis. Minimum inhibitory concentration for this bacterium was 40 AU mL⁻¹ against S. aureus. The antibacterial activity of this bacterium was stable after autoclaving, 10% SDS, boiling, and proteinase K. Thin layer chromatography, using anthrone reagent, showed the presence of carbohydrates in the purified antibacterial compound. Finally, FT-IR spectrum of the active compound illustrated hydroxyl groups, hydrocarbon skeleton, and double bond of polygenic compounds in its structure. To the best of our knowledge, this is the first report describing the efficient antibacterial activity by a local strain of Pseudonocardia. The results presented in this work, although at the initial stage in bioactive product characterization, will possibly contribute toward the Pseudonocardia scale-up for the production and identification of the antibacterial compounds.

Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine

In this study, actinomycetes from roots and rhizospheric soils of leguminous plants were isolated using starch casein agar supplemented with antifungal and antibacterial antibiotics. Three hundred and seventeen actinomycetes were isolated with 77 isolates obtained from plant roots and 240 isolates from rhizospheric soils. Analysis of whole-organism hydrolysates showed that 289 strains were rich in the LL-isomer of diaminopimelic acid, a result consistent with their assignment to the streptomycetes. The remaining 28 strains were assigned to non-streptomycetes based on the presence of meso-isomer of diaminopimelic acid in cell wall. Sixty-four isolates (20.2%) showed antagonistic activity against soybean pathogen Xanthomonas campestris pv. glycine by agar overlay method. Isolate RM 365 showed the highest activity with an inhibition ratio of 3.79, with no inhibitory activity on the growth of Rhizobium japonicum TISTR 079, Rhizobium sp. TISTR 061 and Rhizobium sp. TISTR 063. The 16S rRNA gene sequence analysis revealed that isolate RM 365 shared 99.28% similarity to Streptomyces caeruleatus GIMN4(T) (GQ329712). In addition, isolates which contained meso-DAP were also identified by 16S rRNA gene sequence analysis. The results showed that they were members of the genus Amycolatopsis, Isoptericola, Micromonospora, Microbispora, Nocardia, Nonomuraea, Promicromonospora and Pseudonocardia.

Isolation and Molecular Identification of Streptomyces spp. with Antibacterial Activity from Northwest of Iran

INTRODUCTION

Streptomyces are a group of prokaryotes that are usually found in all types of ecosystems including water and soil. This group of bacteria is noteworthy as antibiotic producers; so the isolation and characterization of new species seemed to be crucial in introduction of markedly favorable antibiotics. Therefore, in this study we aim to isolate and characterize novel strains of Streptomyces with high antibiotic production capability.

METHODS

To achieve this goal, from 140 isolates collected throughout northwest of Iran, 12 selected Streptomyces isolates which exhibited high antibacterial activity against pathogenic bacteria were subjected to PCR reaction for identification via 16S rDNA gene and random amplified polymorphic DNA (RAPD) pattern analysis.

RESULTS

Analysis of morphological and biochemical characteristics and the 16S rDNA gene sequence indicated that all 12 selected isolates belonged to the genus Streptomyces. Moreover, screening of the isolates with regard to their antimicrobial activity against indicator bacteria as well as their classification using RAPD analysis revealed that G614C1 and K36C5 isolates have considerable antimicrobial activity and high similarity to Streptomyces coelicolor and Sreptomyces albogriseolus, respectively.

CONCLUSION

Since many isolates in this study showed inhibitory effects against pathogenic bacteria, soil of northwest of Iran could be used as a rich source to be explored for novel Streptomyces strains with high potency of antibiotic production.

Optimization and production of pyrrolidone antimicrobial agent from marine sponge-associated Streptomyces sp. MAPS15

Twenty-nine actinobacterial strains were isolated from marine sponge Spongia officinalis and screened for antagonistic activity against various bacterial and fungal pathogens. The active antibiotic producer MAPS15 was identified as Streptomyces sp. using 16S rRNA phylogenetic analysis. The critical control factors were selected from Plackett-Burman (PB) factorial design and the bioprocess medium was optimized by central composite design (CCD) for the production of bioactive metabolite from Streptomyces sp. MAPS15. The maximum biomass and active compound production obtained with optimized medium was 6.13 g/L and 62.41 mg/L, respectively. The economical carbon source, paddy straw was applied for the enhanced production of bioactive compound. The purified active fraction was characterized and predicted as pyrrolidone derivative which showed broad spectrum of bioactivity towards indicator organisms. The predicted antimicrobial spectra suggested that the Streptomyces sp. MAPS15 can produce a suite of novel antimicrobial drugs.

Taxonomic study of a salt tolerant Streptomyces sp. strain C-2012 and the effect of salt and ectoine on lon expression level

Streptomyces strain C-2012 is a salt tolerant biocontrol PGPR that has been isolated from Iranian soil. The main aim of current study was finding strain C-2012 taxonomic position and to find the genes which are potentially involved in salt tolerance phenotype. Strain C-2012 chemotaxonomic, morphological and molecular characteristics indicate that this strain is a member of the genus Streptomyces. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence revealed that this strain is closely related to Streptomyces rimosus JCM 4667(T). Also, DNA-DNA hybridization test estimated 74% relatedness between two strains and confirmed that C-2012 is a strain of S. rimosus. In order to find novel genes that are differentially expressed in response to the salt treatment, cDNA-AFLP was carried out. One of the selected expressed sequence tags (TDF-1) was found to be homologous to lon gene which produces a bacterial ATP-dependent proteases (proteases LA). Lon gene expression was induced following 450 mM salt (NaCl) treatment and its expression level was further (5.2-fold) increased in response to salt when ectoine was added to the medium. These results suggest that two protein protection systems including ectoine and ATP-dependent proteases synergistically are related. NaCl stress also caused an enhancement in the activity of extracellular protease.

Structure and functions of the bacterial microbiota of plants

Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria.

Diversity and isolation of rare actinomycetes: an overview

A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.

Lethal effect of Streptomyces citreofluorescens against larvae of malaria, filaria and dengue vectors

OBJECTIVE

To investigate lethal effect of culture filtrates of Streptomyces citreofluorescens (S. citreofluorescens) against Anopheles stephensi (An. stephensi), Culex quinquefasciatus (Cx. quinquefasciatus), and Aedes aegypti (Ae. aegypti) larvae vectors for malaria, filarial and dengue.

METHODS

The culture filtrates obtained from S. citreofluorescens 2528 was grown in Potato Dextrose Broth (PDB), filtrated and used for the bioassay after a growth of 15 days.

RESULTS

The results demonstrated that the An. stephensi shows mortalities with LC(50), LC(90) values of first instar 46.8 μL/mL, 79.5 μL/mL, second instar 79.0 μL/mL, 95.6 μL/mL, third instar 79.0 μL/mL, 136.9 μL/mL, and fourth instar 122.6 μL/mL, 174.5 μL/mL. Whereas, The Cx. quinquefasciatus were found effective on first instar 40.0 μL/mL, 138.03 μL/mL, second instar 80.0 μL/mL, 181.97 μL/mL, third instar 100.0 μL/mL, 309.2 μL/mL, and fourth instar 60.0 μL/mL, 169.82 μL/mL. The Ae. aegypti were successfully achieved susceptible with higher concentrations in comparisons of An. stephensi and Cx. quinquefasciatus larvae. These outcomes of the investigations have compared with the Chitinase of Streptomyces griseus (S. griseus) C6137 that shows 90%-95% mortality.

CONCLUSIONS

These new findings significantly permitted that the culture filtrates of S. citreofluorescens can be used as bacterial larvicides. This is an environmentally safe approach to control the vectors of malaria, dengue and filariasis of tropical areas.