Isolation, phylogenetic analysis and antimicrobial activity of halophilic actinomycetes from different saline environments located near Çorum province

Nocardiopsis codii sp. nov., and Rhodococcus chondri sp. nov., two novel actinomycetal species isolated from macroalgae collected in the northern Portuguese coast

Two novel actinomycetal strains, designated CC-R113T and CC-R104T, were isolated from the tissues of two macroalgae collected on the northern Portuguese coast. Phylogenetic analyses based on the 16S rRNA gene showed that strain CT-R113T belongs to the genus Nocardiopsis, being closely related to Nocardiopsis umidischolae 66/93T and Nocardiopsis tropica VKM Ac-1457T, with 98.65 and 98.39 % sequence similarity, respectively. The clade formed between the three type strains was confirmed by phylogenomic analysis. The genome of strain CT-R113T was 7.27 Mb in size with a G+C content of 71.3 mol %, with average nucleotide identity (ANI) values of 89.59 and 90.14 % with strains 66/93T and VKM Ac-1457T, respectively. The major cellular fatty acids were identified as C18 : 1  ω9c, iso-C16 : 0 and anteiso-C17 : 0. Menaquinone 10 (MK-10) was the major respiratory quinone. Comparative analysis of 16S rRNA gene sequences showed that strain CC-R104T belongs to the genus Rhodococcus and is most closely related to Rhodococcus pyridinivorans DSM 44555T, with 98.24 % sequence similarity. However, phylogenomic analysis revealed that strain CC-R104T establishes a clade with Rhodococcus artemisae DSM 45380T, being more distant from Rhodococcus pyridinivorans DSM 44555T. The genome of strain CC-R104T was 5.34 Mb in size with a G+C content of 67.01 mol%. The ANI value between strains CC-R104T and DSM 45380T was 81.2 % and between strains CC-R104T and DSM 44555T was 81.5 %. The major cellular fatty acids were identified as C18 : 1  ω9c, C16 : 0 and summed feature 3. Menaquinone 8 (MK-8) was the only respiratory quinone. For both CC-R113T and CC-R104T, optimum growth was observed at pH 7.0, 28 °C and 0-5 % NaCl and whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid. On the basis of phenotypic, molecular and chemotaxonomic characteristics, strains CT-R113T and CC-R104T are considered to represent novel species, for which the names Nocardiopsis codii sp. nov. (type strain CT-R113T=LMG33234T=UCCCB172T) and Rhodococcus chondri sp. nov. (type strain CC-R104T=LMG33233T=UCCCB171T) are proposed.

Three nona-2,7-dienoic acid derivatives from saltern derived Micromonospora sp. FXY415

Three new compounds, apocimycin A-C, were identified from a saltern-derived Micromonospora sp. strain FXY415, isolated from Dongshi saltern, Fujian, China. Their planar structures and relative configuration were confirmed mainly by analysis of 1D- and 2D- NMR spectra. Three compounds belong to 4,6,8-trimythyl nona-2,7-dienoic acid derivatives, apocimycin A also has a phenoxazine nucleus. Apocimycin A-C exhibited weak cytotoxic and antimicrobial activities. Our research showed again that microbial communities in extreme environments are a potential resource in looking for new and bioactive led compounds.

Alternative protocol leading to rapid identification of Actinomycetes isolated from Algerian desertic soil by MALDI-TOF mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium. This protocol includes incubation of colony removed from agar plate with the beta-agarase enzyme, followed by a mechanical lysis and two washes by phosphate buffer and ethanol. Twenty-four Streptomyces and two Lentzea strains isolated from Algerian desertic soils were first identified by 16S rRNA sequencing as gold standard method, rpoB gene was used as a secondary gene target when 16S rRNA did not allow species identification. In parallel the isolates were identified by using the MALDI-TOF MS protocol as reported. After the expansion of the database with the inclusion of this MSPS, the strains were analyzed again in MALDI Biotyper, and all were identified. This work demonstrates that the rapid identification of Actinomycetes can be obtained without protein extraction step frequently used in MALDI-TOF mass spectrometry with this type of microorganisms.

Occurrence of Streptomyces tauricus in mangrove soil of Mangalore region in Dakshina Kannada as a source for antimicrobial peptide

Microbial resistance and deprivation of the effective drugs have become the foremost problem that propels to seek out for advanced approach. This concept initiated a need to search for more effective antimicrobial compounds from reliable sources. The Streptomyces is grouped under phylum Actinobacteria and are considered prolific producers of antibiotics, around 70% of presently available antibiotics are contributed by Streptomyces alone. In this study, Mangroves of the Mangalore Coast offered a unique source for screening Actinomyces group of microorganisms. We investigated on the four soil samples collected from Mangrove swamps of Mangalore, Karnataka, India. Based on their culture traits, the 18 distinct Actinomyces isolates were analyzed through a series of morphological and biochemical tests on starch casein nitrate (SCN) media. Culture biomasses were subjected for intracellular protein extraction through acetone precipitation method; the extracted proteins from each Actinomyces isolate were examined for antimicrobial activity against test organisms. The isolate ANTB-YKMU4 showed potential antimicrobial activity against significant number of test organisms; Bacillus cereus, Proteus vulgaris, Staphylococcus aureus, Salmonella typhimurium, and Pseudomonas aeruginosa. The isolate ANTB-YKMU4 through 16 s rRNA gene sequence analysis was identified as Streptomyces tauricus strain with GenBank accession no. MW785875.1. The S. tauricus further cultivated for efficient biomass growth on SCN media for subsequent protein extraction and purification by a series of Electrophoretic and chromatographic techniques. Thus, by intracellular extractions from S. tauricus resulted in the identification of peptide with a molecular weight of 266 Da that was characterized by LC-MS.

Bioactive protein hydrolysates obtained from amaranth by fermentation with lactic acid bacteria and Bacillus species

Protein hydrolysates are a promising source of bioactive peptides. One strategy by which they can be obtained is fermentation. This method uses the proteolytic system of microorganisms to hydrolyze the parental protein. Fermentation is a little-explored method for obtaining protein hydrolysates from amaranth. Different strains of lactic acid bacteria (LAB) and Bacillus species isolated from goat milk, broccoli, aguamiel, and amaranth flour were used in this work. First, the total protein degradation (%TPD) of amaranth demonstrated by the strains was determined. The results ranged from 0 to 95.95%, the strains that produced a higher %TPD were selected. These strains were identified by molecular biology and were found to correspond to the genera Enterococcus, Lactobacillus, Bacillus, and Leuconostoc. Fermentation was carried out with amaranth flour and the selected strains. After this process, water/salt extracts (WSE) containing the released protein hydrolysates were obtained from amaranth doughs. The peptide concentration was measured by the OPA method. The antioxidant, antihypertensive and antimicrobial activity of the WSE was evaluated. In the FRAP test, the best WSE was LR9 with a concentration of 1.99 μMTE/L ± 0.07. In ABTS, 18C6 obtained the highest concentration with 19.18 μMTE/L ± 0.96. In the DPPH test, there was no significant difference. In terms of antihypertensive activity, inhibition percentages ranging from 0 to 80.65% were obtained. Some WSE were found to have antimicrobial properties against Salmonella enterica and Listeria monocytogenes. Fermentation of amaranth with LAB and Bacillus spp. allowed the release of protein hydrolysates with antioxidant, antihypertensive, and antimicrobial activity.

Diversity of actinomycete and their metabolites isolated from Howz Soltan Lake, Iran

Saline environments are largely unexplored sources of actinomycetes with the potential to produce biologically active secondary metabolites. A total of 34 actinomycete isolates from water, sediments and mostly rhizosphere (82%) were collected from different sites at Howz Soltan Lake in Iran. Based on phylogenetic analysis, the isolates belonged to the genera Streptomyces, Nocardia and Saccharomonospora. Cytotoxic assay revealed extract from isolate act9 as the most potent (19.716±5.72 µg/ml) against the MDA-MB-231 human breast cancer cell. Also, 38% of the isolates showed antimicrobial activity against some of the test microorganisms. The ethyl-acetate extract of isolate act18 showed the strongest antibacterial effect against Staphylococcus aureus and MRSA, and was further analyzed by GC/MS. Ar-tumerone (26.41%) and butyl isodecyl phthalate (21.77 %) were the main constituents detected in the extract. This is the first time Ar-tumerone is being detected in a prokaryote. Isolate act18 showed a high 16S rRNA sequence similarity to that of Streptomyces youssoufiensis DSM 41920. In addition, a number of the isolates produced different enzymes including lipase, amylase, protease, gelatinase, urease and lecithinase. Some of the isolates belonging to the genera Streptomyces and Nocardia exhibited plant growth promoting activity such as increased seed germination, stem length and the number of Echium leaves during the 20 days. Findings from this study indicated the diversity and biosynthetic potential of actinomycetes from saline environment.

Actinomycete Potential as Biocontrol Agent of Phytopathogenic Fungi: Mechanisms, Source, and Applications

Synthetic fungicides have been the main control of phytopathogenic fungi. However, they cause harm to humans, animals, and the environment, as well as generating resistance in phytopathogenic fungi. In the last few decades, the use of microorganisms as biocontrol agents of phytopathogenic fungi has been an alternative to synthetic fungicide application. Actinomycetes isolated from terrestrial, marine, wetland, saline, and endophyte environments have been used for phytopathogenic fungus biocontrol. At present, there is a need for searching new secondary compounds and metabolites of different isolation sources of actinomycetes; however, little information is available on those isolated from other environments as biocontrol agents in agriculture. Therefore, the objective of this review is to compare the antifungal activity and the main mechanisms of action in actinomycetes isolated from different environments and to describe recent achievements of their application in agriculture. Although actinomycetes have potential as biocontrol agents of phytopathogenic fungi, few studies of actinomycetes are available of those from marine, saline, and wetland environments, which have equal or greater potential as biocontrol agents than isolates of actinomycetes from terrestrial environments.

Biodegradation and optimization of bilge water in a sequencing batch reactor using response surface methodology

Bilge water is a significant source of pollution in the marine environment and has captured widespread international attention. In this study, a sequencing batch reactor (SBR) combined with strain S2 identified as Bacillus licheniformis was employed to assess the biodegradation of Chemical Oxygen Demand (COD) from bilge water. The influencing variables such as temperature, pH level and inoculum concentration on the performance SBR system were optimized by utilizing response surface methodology (RSM). The experimental results showed that the maximum COD removal of 77.81% was reached at the optimal SBR operation conditions of temperature 35.44 °C pH 8.13, and inoculum concentration 31.47 mL. In the practical application of SBR, it was found that the decrease in hydraulic retention time (HRT) was accompanied by a decrease in COD degradation rate. The biodegradation kinetics of COD in bilge water were well fitted with the first-order equation with a higher R² value of 0.98106. In conclusion, COD in bilge water can be efficiently biodegraded by SBR under the optimization of RSM.

Genus Nocardiopsis: A Prolific Producer of Natural Products

Actinomycetes are currently one of the major sources of bioactive secondary metabolites used for medicine development. Accumulating evidence has shown that Nocardiopsis, a key class of actinomycetes, has the ability to produce novel bioactive natural products. This review covers the sources, distribution, bioactivities, biosynthesis, and structural characteristics of compounds isolated from Nocardiopsis in the period between March 2018 and 2021. Our results reveal that 67% of Nocardiopsis-derived natural products are reported for the first time, and 73% of them are isolated from marine Nocardiopsis. The chemical structures of the Nocardiopsis-derived compounds have diverse skeletons, concentrating on the categories of polyketides, peptides, terphenyls, and alkaloids. Almost 50% of the natural products isolated from Nocardiopsis have been discovered to display various bioactivities. These results fully demonstrate the great potential of the genus Nocardiopsis to produce novel bioactive secondary metabolites that may serve as a structural foundation for the development of novel drugs.

Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens

Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of growth and physiological conditions. Antimicrobial developments from hypersaline environments, such as lagoons, estuaries, and salterns, accommodate several halophilic microbes. Salinity is a distinctive environmental factor that continuously promotes the metabolic adaptation and flexibility of halophilic microbes for their survival at minimum nutritional requirements. A genetic adaptation to extreme solar radiation, ionic strength, and desiccation makes them promising candidates for drug discovery. More microbiota identified via sequencing and ‘omics’ approaches signify the hypersaline environments where compounds are produced. Microbial genera such as Bacillus, Actinobacteria, Halorubrum and Aspergillus are producing a substantial number of antimicrobial compounds. Several strategies were applied for producing novel antimicrobials from halophiles including a consortia approach. Promising results indicate that halophilic microbes can be utilised as prolific sources of bioactive metabolites with pharmaceutical potentialto expand natural product research towards diverse phylogenetic microbial groups which inhabit salterns. The present study reviews interesting antimicrobial compounds retrieved from microbial sources of various saltern environments, with a discussion of their potency in providing novel drugs against clinically drug-resistant microbes.

Isolation and identification of Streptomyces tunisiensis from Garmsar salt cave soil with antibacterial and gene expression activity against Pseudomonas aeruginosa

It is known that more than 70% of the current antibiotics have been produced by Streptomyces; therefore, the main goal of the present study was to isolate halophiles Streptomyces to investigate their antimicrobial properties on the expression of the pathogenic genes of clinically resistant Pseudomonas aeruginosa. To this aim, isolation of Streptomyces from soil was performed by serial dilution method, and cultivation on ISP2 and SCA medium. The secondary metabolite was extracted by ethyl acetate method. The presence of exo A, alg D and oprl genes were determined by PCR in 50 clinical isolates of Pseudomonas aeruginosa. The inhibitory effect of active metabolites on gene expression were investigated by employing the real-time PCR technique. The purification of secondary metabolites were performed by employing the HPLC technique. Moreover, the FTIR technique was employed to determine the functional groups to help performing identifications by employing the LC-MS technique. Finally, selected Streptomyces was identified by 16S ribosomal RNA gene. Accordingly, the possible forms of Streptomyces were isolated and identified, in which Streptomyces number 25 had the highest growth inhibition zone against the clinical strains of Pseudomonas aeruginosa. The obtained results of molecular analysis showed 95.4% similarity to Streptomyces tunisiensis. The effect of selected Streptomyces secondary metabolites reduced expressions of both of exo A and algD genes in 1024μg/mL concentration. In this regard, the potent fraction could be known as an isobutyl Nonactin analogue. The concluding remarks of this work showed the antimicrobial activity of halophilus Streptomyces species against the resistant strains of Pseudomonas aeruginosa with the ability of producing antibiotics proposing for running further investigations to determine the active compound structures.

Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment

AIMS

The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity.

METHODS AND RESULTS

Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown.

CONCLUSION

The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.

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.