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International Journal of Systematic and... May 2022Three strains of members of the family , which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1, HD4P25 and RD4P76, were isolated from...
Three strains of members of the family , which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1, HD4P25 and RD4P76, were isolated from halophytes in Baotou, Inner Mongolia, PR China. A phylogenetic analysis based on the 16S rRNA gene and the whole genome sequences revealed that HD4P25 clustered with YIM 93174 with a similarity of 98.4 %, and RD4P76 shared the highest similarity of 16S rRNA gene with SA4 (97.5 %). M4U3P1 clustered with strains of genera and based on whole-genome sequence analyses, but its 16S rRNA gene had the highest similarity to '' EGI 80668 (96.1 %). The average nucleotide's identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values of the three isolated strains to their close relatives were well below the threshold value for identifying a novel species.On the basis of the phylogenetic, physiological and phenotypic results, gen. nov., sp. nov. [type strain M4U3P1 (=CGMCC 1.17076=JCM 33851)] sp. nov. [type strain HD4P25 (=CGMCC 1.18651 =JCM 34524)] and sp. nov. [type strain RD4P76 (=CGMCC 1.18659=JCM 34525)] were proposed, respectively. All three species are ubiquitous in the bulk saline-alkaline soils, but only the species represented by strain RD4P76 was widely distributed in the rhizosphere soil, the above-ground part and the roots of . The species represented by M4U3P1 can be detected in the roots of , and rarely detected in the above-ground parts of . The species represented by HD4P25 was rarely detected in the interior of . The three strains could inhibit some of the Gram-stain-positive bacteria (i.e. members of the genera , and ) in the saline-alkali soil. A genomic analysis of these three strains revealed that they can synthesize different antagonistic compounds, such as aminobenzoate and bacitracin or subtilisin.
Topics: Bacillaceae; Bacillus; Bacterial Typing Techniques; Base Composition; Chenopodiaceae; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salt-Tolerant Plants; Sequence Analysis, DNA; Soil
PubMed: 35550242
DOI: 10.1099/ijsem.0.005337 -
Biology Mar 2022The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV...
The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m and 6000 J/m UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, sp. TKL1057 and sp. TKL1152 showed higher radiation-resistant capabilities than R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
PubMed: 35453702
DOI: 10.3390/biology11040501 -
Microbial Cell Factories Mar 2022The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed...
BACKGROUND
The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C-carotenoid fatty acid ester produced by Planococcus sp. CP5-4.
RESULTS
Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C-carotenoid fatty acid ester, methyl 5-(6-C)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4.
CONCLUSION
We identified and characterized the carotenoid biosynthetic gene cluster and the C-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
Topics: Carotenoids; Multigene Family; Phylogeny; Planococcus Bacteria; South Africa
PubMed: 35305628
DOI: 10.1186/s12934-022-01752-1 -
Microorganisms Dec 2021Marine bacterial biomineralisation by CaCO precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be...
Marine bacterial biomineralisation by CaCO precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera and . All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, CD6 exhibited the most efficient precipitation of CaCO. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.
PubMed: 35056526
DOI: 10.3390/microorganisms10010076 -
International Journal of Environmental... Jan 2022One cold-adapted strain, named sp. XW-1, was isolated from the Yellow Sea. The strain can produce biosurfactant with petroleum as sole source of carbon at low...
One cold-adapted strain, named sp. XW-1, was isolated from the Yellow Sea. The strain can produce biosurfactant with petroleum as sole source of carbon at low temperature (4 °C). The biosurfactant was identified as glycolipid-type biosurfactant species by thin-layer chromatography (TLC) and Fourier transform infrared spectroscopy (FTIR). It reduced the surface tension of water to 26.8 mN/m with a critical micelle concentration measurement of 60 mg/L. The produced biosurfactant possesses high surface activity at wide ranges of temperature (-18-105 °C), pH values (2-12), and salt concentrations (1-18%). The biosurfactant exhibited higher surface activity and higher growth rate of cells with hexadecane and diesel as carbon source. The strain sp. XW-1 was also effective in degrading crude oil, after 21 days of growth at 4 °C in medium with 1% crude oil and 1% (/) bacteria broth, 54% of crude oil was degraded. The results suggest that sp. XW-1 is a promising candidate for use in the bioremediation of petroleum-contaminated seawater in the Yellow Sea during winter. This study reported for the first time that isolated from the Yellow Sea can produce biosurfactant using petroleum as the sole carbon source at low temperature (4 °C), showing its ecological role in the remediation of marine petroleum pollution.
Topics: Biodegradation, Environmental; Carbon; Petroleum; Spectroscopy, Fourier Transform Infrared; Surface-Active Agents
PubMed: 35055609
DOI: 10.3390/ijerph19020782 -
Archives of Microbiology Jan 2022Oxytetracycline (OTC), is a widely used veterinary antibiotic for treatment and prophylaxis in aquaculture. As an emerging pollutant, OTC in the environment exerts...
Oxytetracycline (OTC), is a widely used veterinary antibiotic for treatment and prophylaxis in aquaculture. As an emerging pollutant, OTC in the environment exerts selective pressure on aquatic organisms causing proliferation of antibiotic resistant genes. In the present study, an OTC tolerant isolate labelled as pw2 was selected among the 11 OTC tolerant isolates, isolated from the aquaculture effluent, for investigating its OTC degrading potential. The cell morphology, biochemical characteristics, and 16S ribosomal RNA (rRNA) gene sequence of the isolated strain indicated that it belonged to the genus Planococcus. The OTC removal percentage was estimated through measuring its residual concentration in the culture medium with high performance liquid chromatography. The strain exhibited maximum removal efficiency of 90.62%, with initial OTC concentration of 10 µg/ml. The optimum degrading conditions were 35 °C and pH 7. The degradation rate of OTC with (biotic) and without strain pw2 (abiotic) was 3.253 and 1.149 mg/l/d, respectively. The half-life was recorded to be 2.13 d in the presence of strain pw2, in contrast to 6.03 days recorded without strain pw2. The total (biotic + abiotic) OTC degradation efficiency was 75.74, 83.93, 90.62, and 86.47% for the initial OTC concentrations of 1 to 25 µg/ml, respectively. Addition of carbon and nitrogen did not influence the OTC removal which indicates Planococcus sp. pw2 use OTC as sole energy source. Thus, Planococcus sp. pw2 plays a vital role in reducing the OTC concentration in the environment, offering a promising method for treatment of aquaculture effluent containing OTC.
Topics: Anti-Bacterial Agents; Aquaculture; Bacteria; Oxytetracycline; RNA, Ribosomal, 16S
PubMed: 34994864
DOI: 10.1007/s00203-021-02732-6 -
BMC Microbiology Oct 2021Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary...
BACKGROUND
Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention.
RESULTS
In this study, a new bacterial strain MSAK28401 from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401 belongs to the genus Planococcus. Cells of this strain were coccoid (0.89-1.05 μm) and aerobic. The majority of the fatty acid content was C anteiso (37.67 ± 0.90%) followed by C ω7c alcohol (10.37 ± 1.22%) and C iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA-DNA hybridization values between the strain MSAK28401 and type strains P. citreus DSM 20549 and P. rifietoensis M8 were lower than 91 and 70%, respectively. The strain MSAK28401 (=KCTC 43283 and MCCC 1k05448) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401 has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill.
CONCLUSIONS
This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401 isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism.
Topics: Animals; Antarctic Regions; Bacterial Proteins; DNA, Bacterial; Euphausiacea; Extremophiles; Fatty Acids; Genome, Bacterial; Nucleic Acid Hybridization; Phenotype; Phylogeny; Planococcus Bacteria; Secondary Metabolism; Sequence Analysis, DNA
PubMed: 34686131
DOI: 10.1186/s12866-021-02347-3 -
Saudi Journal of Biological Sciences Jun 2021Chlorpyriphos is one of the major organophosphorus pesticides used widely to control a range of insect pests across several crops. This insecticide is hazardous to the...
Chlorpyriphos is one of the major organophosphorus pesticides used widely to control a range of insect pests across several crops. This insecticide is hazardous to the environment and toxic to mammals, thus, it is essential to remove the same from the environment. Similarly, use of polythene is also increasing day by day. Therefore, it is highly important to identify ways to degrade chlorpyriphos and other pesticides from the environment. We studied the degradation of chlorpyriphos and polyethylene by Citrus mealybug () bacterial endosymbionts such as and . This investigation revealed that bacterial endosymbionts use the polythene as a source of carbon and solubilize them by their enzymatic machinery. The degradation of polyethylene by endosymbionts showed a significant reduction in weight of polyethylene sheet after 15, 30 and 45 days of treatment. The SEM images showed localized degradation of the polyethylene around the bacterial cells in the biofilm. Further, the tensile strength (percentage elongation) was significantly reduced after 45 days of incubation. The weight of paraffin wax showed significant reduction in . A significant reduction in total amount of chlorpyriphos in soil was observed at an interval of 7, 14 and 21 days after treatment by the bacterial isolates. Among the bacteria, and were found to be most effective. The results from this study show that endosymbionts can be significantly implicated in degrading chlorpyriphos and polyethylene from the environment.
PubMed: 34121858
DOI: 10.1016/j.sjbs.2021.03.058 -
Journal of Hazardous Materials Jul 2021Long-term exposure of anammox process to 1,4-dioxane was investigated using periodic anammox baffled reactor (PABR) under different 1,4-dioxane concentrations. The...
Long-term exposure of anammox process to 1,4-dioxane was investigated using periodic anammox baffled reactor (PABR) under different 1,4-dioxane concentrations. The results generally indicated that PABR (composed of 4 compartments) has robust resistance to 10 mg-dioxane/L. The 1 compartment acted as a shield to protect subsequent compartments from 1,4-dioxane toxicity through secretion of high extracellular polymeric substance (EPS) of 152.9 mg/gVSS at 10 mg-dioxane/L. However, increasing 1,4-dioxane to 50 mg/L significantly inhibited anammox bacteria; e.g., ~ 93% of total nitrogen removal was lost within 14 days. The inhibition of anammox process at this dosage was most likely due to bacterial cell lysis, resulting in the decrease of EPS secretion and specific anammox activity (SAA) to 105.9 mg/gVSS and 0.04 mg N/gVSS/h, respectively, in the 1 compartment. However, anammox bacteria were successfully self-recovered within 41 days after the cease of 1,4-dioxane exposure. The identification of microbial compositions further emphasized the negative impacts of 1,4-dioxane on abundance of C. Brocadia among samples. Furthermore, the development of genus Planococcus in the 1 compartment, where removal of 1,4-dioxane was consistently observed, highlights its potential role as anoxic 1,4-dioxane degrader. Overall, long-term exposure to 1,4-dioxane should be controlled not exceeding 10 mg/L for a successful application.
Topics: Anaerobiosis; Bioreactors; Dioxanes; Extracellular Polymeric Substance Matrix; Fatigue; Humans; Kinetics; Microbial Consortia; Nitrogen; Oxidation-Reduction
PubMed: 34030408
DOI: 10.1016/j.jhazmat.2021.125533 -
The Science of the Total Environment Sep 2021The anaerobic oxidation of methane (AOM) mediated by microorganisms is a key process in the reduction of methane emissions, and AOM-coupled electron acceptors have been...
The anaerobic oxidation of methane (AOM) mediated by microorganisms is a key process in the reduction of methane emissions, and AOM-coupled electron acceptors have been shown to regulate methane emissions into the atmosphere in marine systems. Paddy fields are a significant source of methane and account for 20% of global methane emissions, but the effect of electron acceptors on the methane emission process in flooded paddy fields has been poorly characterized. This study aimed to determine whether the electron acceptors ferric iron and nitrate, and biochar, acting as an electron shuttle, can regulate the AOM process in paddy soil, with or without interaction between biochar and these two electron acceptors. We also aimed to characterize which microorganisms are actively involved. Here, we added C-labeled CH (CH) into anaerobic microcosms to evaluate the role of electron acceptors by measuring the methane oxidation rate and the enrichment of C-labeled CO (CO). We then combined DNA-stable isotope probing with amplicon sequencing to study the active microorganisms. We found for the first time that, in addition to nitrate, ferric iron can also effectively promote AOM in paddy soil. However, there was no significant effect of biochar. Ferric iron-dependent AOM was mainly carried out by iron-reducing bacteria (Geobacter, Ammoniphilus and Clostridium), and nitrate-dependent AOM was mainly by nitrate-reducing bacteria (Rhodanobacter, Paenibacillus and Planococcus). Our results demonstrate that the AOM process, regulated by the electron acceptors ferric iron and nitrate, can alleviate methane emission from paddy soil. The potentially active microorganisms related to electron acceptor reduction may be crucial for this methane sink and deserve further research.
Topics: Anaerobiosis; Archaea; Iron; Methane; Microbiota; Nitrates; Oxidation-Reduction; Soil
PubMed: 34029806
DOI: 10.1016/j.scitotenv.2021.147773