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Ecotoxicology and Environmental Safety Dec 2021Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their...
Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their potentially negative environmental impacts. Recently, the degradability of neonicotinoid in soil has gained more attentions. However, what role soil microbes play in this degradation remains vastly underexplored. In this study, we compared the capacity of soil microbes sampled from different geographic regions and fields to degrade the neonicotinoid insecticide imidacloprid. Additionally, the composition of microbiota having low, middle, and high degradation activity was analyzed via high throughput sequencing. Correlations between microbiota composition and degradation activities were analyzed and reconfirmed. The results showed that the composition of soil microbiota and their degradation activity (ranged from zero to 96.25%) varied significantly between soil samples from different geographic locations. Correlation analysis showed that Paracoccus and Achromobacter bacteria were positively correlated with high degradation activity. Imidacloprid degradation experiments using these bacteria showed that Achromobacter sp. alone exhibited degradation activity reaching and sustaining 100% by day 20 while Paracoccus sp. did not. However, combining these bacteria resulted in increased degradation activity which reached 100% at day 15 relative to that achieved by Achromobacter sp. alone. This study demonstrated the capacity of soil microbes to degrade imidacloprid, and identified two promising bacterial candidates that could be potentially used in future to reduce imidacloprid accumulation in soils.
Topics: Achromobacter; Bacteria; Biodegradation, Environmental; Insecticides; Neonicotinoids; Nitro Compounds; Paracoccus; Soil; Soil Microbiology; Soil Pollutants
PubMed: 34544021
DOI: 10.1016/j.ecoenv.2021.112785 -
Applied and Environmental Microbiology Aug 2021Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as...
Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, sp. 363 and sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of sp. 363 carries three synthase genes and transcribes genes along three PHA pathways (I to III), whereas sp. 392 carries only one gene and transcribes genes along one pathway (I). Thus, sp. 363 has a versatile repertoire of genes and pathways enabling production of both short- and medium-chain-length PHA products. Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, sp. 363 and sp. 392, are able to produce various types of PHA from inexpensive carbon sources. sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.
Topics: Bacterial Proteins; Cold Temperature; Genome, Bacterial; Halomonas; Ice Cover; Paracoccus; Phylogeny; Polyhydroxyalkanoates; Seawater; Temperature
PubMed: 34160268
DOI: 10.1128/AEM.00929-21 -
Applied Microbiology and Biotechnology Mar 2020Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked... (Review)
Review
Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.
Topics: Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Membrane Proteins; Paracoccus denitrificans; Quorum Sensing
PubMed: 32002601
DOI: 10.1007/s00253-020-10400-w -
International Journal of Molecular... Mar 2016His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs). An overview is presented on various surfaces ranging from flat to... (Review)
Review
His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs). An overview is presented on various surfaces ranging from flat to spherical and modified with linker molecules with nitrile-tri-acetic acid (NTA) terminal groups to bind his-tagged proteins in a strict orientation. The bound proteins are submitted to in situ dialysis in the presence of lipid micelles to form a so-called protein-tethered bilayer lipid membrane (ptBLM). MRPs, such as the cytochrome c oxidase (CcO) from R. sphaeroides and P. denitrificans, as well as photosynthetic reactions centers (RCs) from R. sphaeroides, were thus investigated. Electrochemical and surface-sensitive optical techniques, such as surface plasmon resonance, surface plasmon-enhanced fluorescence, surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced resonance Raman spectroscopy (SERRS), were employed in the case of the ptBLM structure on flat surfaces. Spherical particles ranging from µm size agarose gel beads to nm size nanoparticles modified in a similar fashion were called proteo-lipobeads (PLBs). The particles were investigated by laser-scanning confocal fluorescence microscopy (LSM) and UV/Vis spectroscopy. Electron and proton transfer through the proteins were demonstrated to take place, which was strongly affected by the membrane potential. MRPs can thus be used for biosensing purposes under quasi-physiological conditions.
Topics: Bacterial Proteins; Biomimetics; Biosensing Techniques; Electrochemical Techniques; Electron Transport Complex IV; Immobilized Proteins; Lipid Bilayers; Oxidation-Reduction; Paracoccus denitrificans; Photosynthetic Reaction Center Complex Proteins; Rhodobacter sphaeroides; Spectrophotometry, Infrared; Spectrum Analysis, Raman; Surface Plasmon Resonance
PubMed: 26950120
DOI: 10.3390/ijms17030330 -
Bacteriological Reviews Mar 1977
Review
Topics: Adenosine Triphosphatases; Adenosine Triphosphate; Aerobiosis; Anaerobiosis; Azotobacter; Bacteria; Cell Membrane; Cytochromes; Cytoplasm; Electron Transport; Escherichia coli; Mutation; Oxidative Phosphorylation; Paracoccus denitrificans
PubMed: 140652
DOI: 10.1128/br.41.1.47-99.1977 -
Biochimica Et Biophysica Acta Jan 2002An overview of the present knowledge about succinate:quinone oxidoreductase in Paracoccus denitrificans and Bacillus subtilis is presented. P. denitrificans contains a... (Comparative Study)
Comparative Study Review
An overview of the present knowledge about succinate:quinone oxidoreductase in Paracoccus denitrificans and Bacillus subtilis is presented. P. denitrificans contains a monoheme succinate:ubiquinone oxidoreductase that is similar to that of mammalian mitochondria with respect to composition and sensitivity to carboxin. Results obtained with carboxin-resistant P. denitrificans mutants provide information about quinone-binding sites on the enzyme and the molecular basis for the resistance. B. subtilis contains a diheme succinate:menaquinone oxidoreductase whose activity is dependent on the electrochemical gradient across the cytoplasmic membrane. Data from studies of mutant variants of the B. subtilis enzyme combined with available crystal structures of a similar enzyme, Wolinella succinogenes fumarate reductase, substantiate a proposed explanation for the mechanism of coupling between quinone reductase activity and transmembrane potential.
Topics: Amino Acid Sequence; Bacillus subtilis; Bacterial Proteins; Carboxin; Drug Resistance, Microbial; Electron Transport Complex II; Enzyme Inhibitors; Hydroxyquinolines; Intracellular Membranes; Membrane Potentials; Membrane Proteins; Molecular Sequence Data; Multienzyme Complexes; Oxidoreductases; Paracoccus denitrificans; Quinone Reductases; Sequence Alignment; Succinate Dehydrogenase
PubMed: 11803018
DOI: 10.1016/s0005-2728(01)00231-6 -
Current Issues in Molecular Biology 2019Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of... (Review)
Review
Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of methanol or methylamine. The growing availability of genome sequence data has made it possible to investigate methylotrophy in other . The examination of a large number of spp. genomes reveals great variability in C1 metabolism, which have been shaped by different evolutionary mechanisms. Surprisingly, the methylotrophy schemes of many strains appear to have quite different genetic and biochemical bases. Besides the expected 'autotrophic methylotrophs', many strains of this genus possess another C1 assimilatory pathway, the serine cycle, which seems to have at least three independent origins. Analysis of the co-occurrence of different methylotrophic pathways indicates, on the one hand, evolutionary linkage between the Calvin cycle and the serine cycle, and, on the other hand, that genes encoding some C1 substrate-oxidizing enzymes occur more frequently in association with one or the other. This suggests that some genetic module combinations form more harmonious enzymatic sets, which act with greater efficiency in the methylotrophic process and thus undergo positive selection.
Topics: Alphaproteobacteria; Biodiversity; Biological Evolution; Genome, Bacterial; Metabolic Networks and Pathways; Methanol; Methylamines; Oxidation-Reduction; Paracoccus
PubMed: 31166188
DOI: 10.21775/cimb.033.117 -
Journal of Bacteriology Apr 2023The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic...
The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either (one of two homologs in the P. denitrificans genome) or / (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The and / genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second homolog () and / have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.
Topics: Nitrates; Paracoccus denitrificans; Guanosine Tetraphosphate; Nitrous Oxide; Nitric Oxide; Nitrate Reductase; Nitrate Reductases; Respiration; Butyrates
PubMed: 36920204
DOI: 10.1128/jb.00027-23 -
Frontiers in Public Health 2021Disinfection is a key element in controlling infections. Fogging, also known as fumigation, is one of the most effective chemical disinfection methods. Peracetic acid...
Disinfection is a key element in controlling infections. Fogging, also known as fumigation, is one of the most effective chemical disinfection methods. Peracetic acid (PAA) is a powerful oxidant with bactericidal and fungicidal properties. The aim of this study is to determine the type of bacteria and fungi present in educational institutions and whether disinfection by PAA fumigation in these institutions is also effective and useful, as demonstrated previously in healthcare centers. This study was carried out in five kindergartens and five primary schools in Bialystok, Poland. Three rooms have been selected in each of these educational institutions, and the disinfection was carried out in 30 rooms in total. Fogging with PAA was performed in selected rooms. Before and after disinfection, samples were collected from four surfaces: walls, tables, doors, and chair backs. Most frequently detected microorganisms in schools and kindergartens were ssp. . In addition, ssp. were the most prevalent in kindergartens, whereas was the most prevalent in schools. Comparison of the bacterial flora of schools and kindergartens showed statistically significant differences in the prevalence of bacteria on different surfaces. A significant decrease in the number of colonies after disinfection was observed on all surfaces ( < 0.05). In addition, the calculated effectiveness of disinfection was 99.7% in kindergartens and 99.3% in schools. The results indicate that fogging of PAA is a highly effective method of surface disinfection in kindergartens and schools.
Topics: Acinetobacter; Actinobacteria; Micrococcaceae; Paracoccus; Peracetic Acid; Schools; Staphylococcus
PubMed: 34604154
DOI: 10.3389/fpubh.2021.697917 -
Molecules (Basel, Switzerland) Feb 2020Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in... (Review)
Review
Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in agricultural practices has led to environmental toxicity and human health issues. Oxidation, incineration, adsorption, and microbial degradation methods have been developed to remove insecticidal residues from soil/water environments. Compared with physicochemical methods, biodegradation is considered to be a cost-effective and ecofriendly approach to the removal of pesticide residues. Therefore, micro-organisms have become a key component of the degradation and detoxification of methomyl through catabolic pathways and genetic determinants. Several species of methomyl-degrading bacteria have been isolated and characterized, including , , , , , , , , and . The degradation pathways of methomyl and the fate of several metabolites have been investigated. Further in-depth studies based on molecular biology and genetics are needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of methomyl. In this review, we highlight the mechanism of microbial degradation of methomyl along with metabolic pathways and genes/enzymes of different genera.
Topics: Adsorption; Alcaligenes; Bacillus; Biodegradation, Environmental; Cholinesterase Inhibitors; Flavobacterium; Humans; Incineration; Insecticides; Metabolic Networks and Pathways; Methomyl; Oxidation-Reduction; Paracoccus; Pseudomonas; Serratia; Soil Pollutants; Trametes; Water Pollutants, Chemical
PubMed: 32046287
DOI: 10.3390/molecules25030738