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Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
Journal of Biotechnology May 2022The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation...
The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation technique. Based on the concept that bacteria with biomineralization capacity could be effective CaCO inductance agents, this study aimed to evaluate the simultaneous influence of 11 operational and environmental factors on the MICP process, for the first time. Therefore, Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis, isolated from alkaline soils, were used in the selection of the best performing bacterium compared with a well-known MICP bioagent Sporosarcina pasteurii DSM 33. Plackett-Burman's experimental design was labouring to screen all independent variables for their significances on five outputs (pH value, number of viable cells and spores, amount of urea and CaCO precipitate). According to experimentally obtained data, an artificial neural network model based on the Broyden-Fletcher-Goldfarb-Shanno algorithm showed good prediction capabilities, while differences in the relative influences were observed at the bacterial strain level. B. licheniformis turn out to be the most potent bioagent, with a maximum amount of CaCO precipitate of 3.14 g/100 mL in the optimal conditions.
Topics: Bacillus; Bacteria; Biomineralization; Calcium Carbonate; Chemical Precipitation; Soil; Sporosarcina
PubMed: 35427694
DOI: 10.1016/j.jbiotec.2022.04.002 -
Antonie Van Leeuwenhoek Jun 2022A Gram-stain-positive, orange-pigmented, rod-shaped and flagellated bacterial strain T12 was isolated from wetland soil in Kunyu Mountain Wetland in Yantai, China. The...
A Gram-stain-positive, orange-pigmented, rod-shaped and flagellated bacterial strain T12 was isolated from wetland soil in Kunyu Mountain Wetland in Yantai, China. The strain was able to grow at 15-40 °C (optimum 37 °C), at 0.0-9.0% NaCl (optimum 2%, w/v) and at pH 5.5-9.0 (optimum 8.5). A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain T12 is a member of the family Planococcaceae, sharing 97.6% and 97.1% sequence similarity with the type strains of Jeotgalibacillus salarius and Jeotgalibacillus marinus, respectively. Genome-based analyses revealed a genome size of 3,506,682 bp and a DNA G + C content of 43.7%. Besides, the genome sequence led to 55.0-74.6% average amino acid identity values and 67.8-74.7% average nucleotide identity values between strain T12 and the current closest relatives. Digital DNA-DNA hybridization of strain T12 with the type strains of Jeotgalibacillus proteolyticus and J. marinus demonstrated 19.0% and 20.3% relatedness, respectively. The chemotaxonomic analysis showed that the sole quinone was MK-7. The predominant cellular fatty acids were iso-C, anteiso-C, Cω7c alcohol and iso-C. The polar lipids consisted of an unidentified aminolipid, phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. Based on the polyphasic characterization, strain T12 is considered to represent a novel species, for which the name Jeotgalibacillus aurantiacus sp. nov. is proposed. The type strain is T12 (= KCTC 43296 = MCCC 1K07171).
Topics: Bacterial Typing Techniques; Carotenoids; China; Citrus sinensis; DNA, Bacterial; Fatty Acids; Multigene Family; Phospholipids; Phylogeny; Planococcaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Wetlands
PubMed: 35396624
DOI: 10.1007/s10482-022-01731-x -
Biomolecules Feb 2022Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo...
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16-20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5'-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
Topics: Argonaute Proteins; Bacteria; Bacterial Proteins; DNA; Endonucleases; Planococcaceae; RNA
PubMed: 35327547
DOI: 10.3390/biom12030355 -
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 -
Environmental Science and Pollution... Jul 2022Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites...
Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites is not explored yet. This study includes investigation of bio-mediated calcite precipitation for strength improvement and immobilization of heavy metals, specifically lead (Pb), zinc (Zn), and hexavalent chromium (Cr(VI)), in contaminated soils. Firstly, the toxicity resistance of bacteria against different concentrations (1000, 2000, 3000, 4000, and 5000 mg/l) of each heavy metals was investigated and observed that Pb and Cr were less toxic to Sporosarcina pasteurii than Zn. The poorly graded sand was spiked with 333-2000 mg/kg concentrations of a selected individual or mixed metal solutions, i.e., 1000 mg/kg and 2000 mg/kg individual concentrations of Pb, Zn, and Cr(VI); 500 mg/kg and 1000 mg/kg concentration of each metal in "Pb and Zn," "Pb and Cr(VI)," and "Zn and Cr(VI)" mixture of heavy metals; and 333 mg/kg and 666 mg/kg concentration of each metal in "Pb, Zn, and Cr(VI)" mixed metal concentration. Contaminated soil was biotreated with Sporosarcina pasteurii and cementation (a solution of urea and calcium chloride dihydrate) solutions for 18 days. Biocemented sand specimens were subjected to testing of hydraulic conductivity, ultrasonic pulse velocity (UPV), unconfined compressive strength (UCS), calcite content, pH, toxicity characteristic leaching procedure (TCLP), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The heavy metal contaminated samples showed decrease in hydraulic conductivity and increase in UPV and UCS after biotreatment; however, the changes in engineering properties were found more moderate than clean biocemented sand. The conversion of Cr(VI) to Cr(III) followed by CrO precipitation in calcite lattice was observed. Zn was precipitated as smithsonite (ZnCO), while no Pb precipitate was identified in XRD results. TCLP leaching showed Pb and Cr immobilized proportional to calcite precipitated amount, and higher calcite amounts yielded levels within regulatory limits. Pb and Cr(VI) immobilization up to 92 % and 94 % was achieved, respectively, in contaminated biocemented sand. Zn was found completely leachable as smithsonite is only stable down to pH~5, and strongly acidic TCLP solution reversed all immobilization at natural soil pH~8-9.
Topics: Calcium Carbonate; Industrial Waste; Metals, Heavy; Sand; Soil; Soil Pollutants; Sporosarcina; Zinc
PubMed: 35253104
DOI: 10.1007/s11356-022-19551-x -
Gene May 2022The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the...
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C-C, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 10 J/m UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
Topics: Base Composition; Biodegradation, Environmental; Genome Size; Genome, Bacterial; Petroleum; Phylogeny; Planococcaceae; Soil Microbiology; Tibet; Whole Genome Sequencing
PubMed: 35240255
DOI: 10.1016/j.gene.2022.146368 -
International Journal of Systematic and... Feb 2022A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210, was isolated from a saline soil sample collected from Lingxian County, Shandong...
A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of NCIMB 8841 (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAM9210 and the type strain of the most closely related species NCIMB 8841 were 73.6 and 20.6 %, respectively. Strain LAM9210 was found to grow at 10-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 9.0) and with 0-6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C and iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210 contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LAM9210 (=CGMCC 1.18607=GDMCC 1.2002=JCM 32514).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Soil; Soil Microbiology; Sporosarcina; Vitamin K 2
PubMed: 35171090
DOI: 10.1099/ijsem.0.005244 -
Environmental Science and Pollution... Jun 2022In this study, the feasibility of Cr(VI) removal from synthetic groundwater by bio-permeable reactive barrier constructed from novel iron-based material (SiO/nano-FeCO...
In this study, the feasibility of Cr(VI) removal from synthetic groundwater by bio-permeable reactive barrier constructed from novel iron-based material (SiO/nano-FeCO composite, SNFC) and Sporosarcina saromensis W5 was investigated. According to breakthrough study, an enhanced Cr(VI) removal was found in Bio-SNFC column. The Cr(VI) removal performances of biotic column with 0.2 g biomass and 0.4 g biomass were 16.2 mg/g and 17.9 mg/g, respectively, which were 19.6% and 32.1% higher than that of abiotic column (13.5 mg/g). However, excessive biomass (0.9 g) would cause pore clogging and have a negative impact on the Cr(VI) removal performance of the biotic column, whose removal capability (29.1%) was lower than that of abiotic column. The introduction of proper microorganisms enhanced the utilization of iron and enabled a higher proportion of Fe(II) in biotic column, which provided more reactive sites for Cr(VI) removal. The solid phase characterization indicated the generation of Fe(III) oxide/hydroxide on SNFC surface. The removal of Cr(VI) in Bio-SNFC column was depended on reduction-precipitation, and the final products related to chromium were mainly Cr(OH) and CrO. The present work provides a new and sustainable remediation technology for in situ bioremediation of Cr(VI)-contaminated groundwater.
Topics: Bioreactors; Chromium; Groundwater; Iron; Silicon Dioxide; Sporosarcina; Water Pollutants, Chemical
PubMed: 35138543
DOI: 10.1007/s11356-022-18972-y -
Environmental Science and Pollution... Jun 2022Seawater intrusion has a detrimental effect on agriculture, industry, and human health. One question of particular interest is how the microbial community responds to...
Seawater intrusion has a detrimental effect on agriculture, industry, and human health. One question of particular interest is how the microbial community responds to and reflects seawater intrusion with seasonal variation. The current study explored the seasonal changes in bacterial community composition and interaction in the vicinity of Pearl River Estuary in dry season (January) and wet season (September). Results indicated that the salinity of sediment samples obtained in dry season was higher than that in wet season. The salt stress induced a declined alpha diversity but resulted in a loosely connected and unstable biotic interaction network in the bacterial communities. Random forest prediction and redundancy analysis of bacterial community indicated that salinity substantially affected the bacterial communities. Multiple lines of evidence, including the enrichment of bacterial taxa in the high-salinity location, microbe-microbe interactions, environment-microbe interactions, and machine learning approach, demonstrated that the families Moraxellaceae and Planococcaceae were the keystone taxa and were resistant to salt stress, which suggested that both of them can be used as potential biological indicators of monitoring and controlling seawater intrusion in coastal zone areas.
Topics: Bacteria; Environmental Biomarkers; Environmental Monitoring; Fresh Water; Humans; Rivers; Seasons; Seawater
PubMed: 35088267
DOI: 10.1007/s11356-021-18053-6