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International Journal of Systematic and... Aug 2017A bacterial strain, designated gyp-1T, was isolated from a mangrove in Taiwan and characterized using the polyphasic taxonomic approach. Cells of gyp-1T were...
A bacterial strain, designated gyp-1T, was isolated from a mangrove in Taiwan and characterized using the polyphasic taxonomic approach. Cells of gyp-1T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, coccoid or short-rod-shaped and formed cream-coloured colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 5.5-7.0 (optimum, pH 6.0) and with 0-4 % NaCl (optimum, 1-2 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that gyp-1T represented a member of the genus Paracoccus and showed the highest levels of sequence similarity with respect to Paracoccus lutimaris HDM-25T (97.8 %) and Paracoccus aminovorans DM-82T (97.7 %). The major fatty acids (>10 %) of gyp-1T were C18 : 1ω7c and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid and two unidentified phospholipids. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.6 mol%. The DNA-DNA hybridization value for gyp-1T with P. lutimaris HDM-25T and P. aminovorans DM-82T was less than 50 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that gyp-1T should be classified as representing a novel species of the genus Paracoccus, for which the name Paracoccus mangrovi sp. nov. is presented. The type strain is gyp-1T (=BCRC 80920T=LMG 29172T=KCTC 42899T).
Topics: Avicennia; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Nucleic Acid Hybridization; Paracoccus; Phospholipids; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone
PubMed: 28809137
DOI: 10.1099/ijsem.0.001993 -
International Microbiology : the... Mar 2019Lindane contamination in different environmental compartments is still posing a serious threat to our environment and effective measures need to be taken for the...
Lindane contamination in different environmental compartments is still posing a serious threat to our environment and effective measures need to be taken for the detoxification of lindane. Soil bacteria isolated from agricultural fields are known to possess certain plant growth promoting traits like the production of phytohormones, production of ammonia, nitrogen fixation and solubilization of phosphorus, etc. In the present study, an indigenous bacterial strain Paracoccus sp. NITDBR1 have been isolated from an agricultural field in Manipur, India which could grow on 100 mg L lindane as the sole source of carbon and could degrade up to 90% of lindane in mineral salt media under liquid culture conditions in 8 days. The strain NITDBR1 was able to form biofilm in lindane media and the addition of substrate like glucose and sucrose enhanced the biofilm formation by 1.3 and 1.17-fold respectively in 3 days. The strain NITDBR1 could produce glycolipid and glycoprotein based biosurfactants. It was also found to possess plant growth promoting traits like nitrogen fixation and indole-3-acetic acid production to assist crop production. The phytotoxicity studies carried out on mustard seeds revealed that the degradation products formed after treatment with NITDBR1 could lower the toxicity of lindane for root elongation by 1.3-fold. Therefore, strain NITDBR1 could be useful for the bioremediation of soil contaminated with lindane with lesser damage to the environment, biofilm forming ability may help the bacteria survive under stressed environmental conditions, and biosurfactant production will help in increasing the bioavailability of contaminants. The plant growth promoting traits can be beneficial for agriculture. With such soil friendly activities coupled with pesticide degradation, this strain can be used for environmental as well as agricultural applications.
Topics: Biofilms; Biotransformation; Carbon; Environmental Pollutants; Glucose; Glycolipids; Glycoproteins; Hexachlorocyclohexane; India; Indoleacetic Acids; Insecticides; Mustard Plant; Nitrogen Fixation; Paracoccus; Plant Growth Regulators; Plant Roots; Soil Microbiology; Sucrose; Surface-Active Agents
PubMed: 30810939
DOI: 10.1007/s10123-018-00037-1 -
The Science of the Total Environment Sep 2022Bioaerosols have become a major environmental concern in recent years. In this study, the diurnal variations and size distributions of bioaerosols, as well as airborne...
Bioaerosols have become a major environmental concern in recent years. In this study, the diurnal variations and size distributions of bioaerosols, as well as airborne bacterial community compositions and their influencing factors on haze and non-haze days in Xi'an, China, were compared. The results indicated that the mean bacteria and fungi concentrations on non-haze days were 1.7 and 1.4 times of those on haze days, respectively, whereas the mean total airborne microbe (TAM) concentration was higher on haze days. Bacteria concentrations were the lowest in the afternoon, and the TAM concentration exhibited a bimodal distribution with two peaks coinciding with traffic rush hours. On haze days airborne fungi was mainly attached to PM, whereas bacteria and TAM were mainly distributed in coarse PM. The relative abundance of Chao1, Shannon and Simpson indices of bacterial communities were higher in the non-haze day samples, for the reason that high PM levels with a large specific surface area may absorb more toxic and harmful substances on haze days, which should affect microbial growth. At the generic level, the relative abundance of Rhodococcus, Paracoccus, Acinetobacter, and Kocuria on haze days was higher than that on non-haze days, indicating a higher risk of contracting pathogenic pneumonia. The results of the redundancy analysis revealed that PM and water-soluble inorganic ions (WSIIs, NO, SO, and NH) strongly affected the bacterial communities on non-haze days, especially Acinetobacter. The atmospheric oxidation capacity (O) had a significant effect on bacterial communities during haze episodes, which were positively correlated with Paracoccus, Deinococcus, Sphingomonas, and Rubellimicrobium and were negatively correlated with Rhodococcus. These results provide valuable data to elucidate the formation and evolution of bioaerosol between haze and non-haze events and its potential threats to human health.
Topics: Aerosols; Air Microbiology; Air Pollutants; Bacteria; China; Environmental Monitoring; Fungi; Humans; Particle Size; Particulate Matter; Seasons
PubMed: 35588847
DOI: 10.1016/j.scitotenv.2022.155969 -
Biochimica Et Biophysica Acta.... Sep 2018The ATP synthase is a reversible nanomotor that gyrates its central rotor clockwise (CW) to synthesize ATP and in counter clockwise (CCW) direction to hydrolyse it. In... (Review)
Review
The ATP synthase is a reversible nanomotor that gyrates its central rotor clockwise (CW) to synthesize ATP and in counter clockwise (CCW) direction to hydrolyse it. In bacteria and mitochondria, two natural inhibitor proteins, namely the ε and IF subunits, prevent the wasteful CCW FF-ATPase activity by blocking γ rotation at the α/β/γ interface of the F portion. In Paracoccus denitrificans and related α-proteobacteria, we discovered a different natural F-ATPase inhibitor named ζ. Here we revise the functional and structural data showing that this novel ζ subunit, although being different to ε and IF, it also binds to the α/β/γ interface of the F of P. denitrificans. ζ shifts its N-terminal inhibitory domain from an intrinsically disordered protein region (IDPr) to an α-helix when inserted in the α/β/γ interface. We showed for the first time the key role of a natural ATP synthase inhibitor by the distinctive phenotype of a Δζ knockout mutant in P. denitrificans. ζ blocks exclusively the CCW FF-ATPase rotation without affecting the CW-FF-ATP synthase turnover, confirming that ζ is important for respiratory bacterial growth by working as a unidirectional pawl-ratchet PdFF-ATPase inhibitor, thus preventing the wasteful consumption of cellular ATP. In summary, ζ is a useful model that mimics mitochondrial IF but in α-proteobacteria. The structural, functional, and endosymbiotic evolutionary implications of this ζ inhibitor are discussed to shed light on the natural control mechanisms of the three natural inhibitor proteins (ε, ζ, and IF) of this unique ATP synthase nanomotor, essential for life.
Topics: Adenosine Triphosphate; Alphaproteobacteria; Amino Acid Sequence; Enzyme Inhibitors; Mitochondria; Mitochondrial Proton-Translocating ATPases; Paracoccus denitrificans; Protein Conformation; Protein Subunits; Proteins; Sequence Homology; ATPase Inhibitory Protein
PubMed: 29886048
DOI: 10.1016/j.bbabio.2018.06.005 -
Journal of Theoretical Biology Aug 2016We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction...
We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request.
Topics: Aerobiosis; Anaerobiosis; Biomass; Calibration; Denitrification; Models, Theoretical; Paracoccus denitrificans; Stochastic Processes; Thermodynamics
PubMed: 27179457
DOI: 10.1016/j.jtbi.2016.05.017 -
International Journal of Systematic and... Apr 2020An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008, was isolated from the shallow-sea hydrothermal systems off Kueishantao...
An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008, was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China, and it was studied by using a polyphasic taxonomic approach. Cells were Gram-stain-negative, and catalase- and oxidase-positive. Strain TK008 exhibited highest 16S rRNA gene sequence similarity of 97.1 % to F14. The phylogenetic trees based on 16S rRNA gene sequences showed that strain TK008 was a member of the genus . Digital DNA-DNA hybridization values between strain TK008 and two closely related species ( and ) were 20.6 and 20.9 %. The average nucleotide identity values of strain TK008 compared with and were 75.2 and 74.6 % respectively. The major isoprenoid quinone was ubiquinone-10. The predominant fatty acids (>10 %) were summed feature 8 (Cω6 and/or Cω7). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, two unidentified lipids and an unidentified glycolipid. The DNA G+C content of strain TK008 from genomic sequence data was 62.54 mol%. On the basis of polyphasic analysis, strain TK008 represents a novel species, for which the name sp. nov. is proposed. The type strain is TK008 (=CGMCC 1.13898=JCM 33630).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Glycolipids; Hydrothermal Vents; Islands; Nucleic Acid Hybridization; Paracoccus; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone
PubMed: 32101515
DOI: 10.1099/ijsem.0.004068 -
Bioresource Technology Oct 2023Photosynthetic microorganisms in microalgal-bacterial granular sludge offer advantages in wastewater treatment processes. This study examined the effects of light...
Photosynthetic microorganisms in microalgal-bacterial granular sludge offer advantages in wastewater treatment processes. This study examined the effects of light intensity and salinity on microalgal-bacterial granular sludge formation and microbial changes. Activated sludge was inoculated into three bioreactors and operated in batch treatment mode for 100 days under different light intensities (0, 60, and 120 μmol m s) and staged increases in salinity concentration (0, 1, 2, and 3%). Results showed that microalgal-bacterial granular sludge was successfully formed within 30 days, and high light exposure increased algal particle stability and inorganic nitrogen removal (63, 66, 71%), while chemical oxygen demand removal (>95%) was similar across groups. High-throughput sequencing results showed that the critical algae were Chlorella and diatoms, while the main bacteria included Paracoccus and Xanthomarina with high extracellular polymeric substance production. This study aims to enhance the comprehension of MBGS processes in saline wastewater treatment under varying light intensities.
Topics: Sewage; Microalgae; Salinity; Chlorella; Extracellular Polymeric Substance Matrix; Bacteria; Bioreactors; Nitrogen; Waste Disposal, Fluid
PubMed: 37488013
DOI: 10.1016/j.biortech.2023.129534 -
Biotechnology and Bioengineering Mar 2021Nitrous oxide (N O), a potent greenhouse gas, is reduced to N gas by N O-reducing bacteria (N ORB), a process which represents an N O sink in natural and engineered...
Nitrous oxide (N O), a potent greenhouse gas, is reduced to N gas by N O-reducing bacteria (N ORB), a process which represents an N O sink in natural and engineered ecosystems. The N O sink activity by N ORB depends on temperature and O exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N ORB. Four N ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol ) compared with the other tested N ORB (38.3-60.1 kJ mol ) indicates that N ORB can adapt to different temperatures. The O inhibition constants (K ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O exposure result in the growth of ecophysiologically distinct N ORB as N O sinks. This knowledge can help develop a suitable N O mitigation strategy according to the physiologies of the predominant N ORB.
Topics: Nitrous Oxide; Paracoccus denitrificans; Pseudomonas stutzeri; Rhodocyclaceae; Temperature
PubMed: 33305820
DOI: 10.1002/bit.27654 -
Microbiological Research Jan 2021The endophytic bacteria were isolated from coffee roots and seeds in Vietnam and identified with 16S rDNA sequencing as belonging to the Actinobacteria, Firmicutes and...
The endophytic bacteria were isolated from coffee roots and seeds in Vietnam and identified with 16S rDNA sequencing as belonging to the Actinobacteria, Firmicutes and Proteobacteria phyla with the Nocardia, Bacillus and Burkholderia as dominant genera, respectively. Out of the thirty genera recovered from Coffea canephora and Coffea liberica, twelve were reported for the first time in endophytic association with coffee including members of the genera Brachybacterium, Caballeronia, Kitasatospora, Lechevalieria, Leifsonia, Luteibacter, Lysinibacillus, Mycolicibacterium, Nakamurella, Paracoccus, Sinomonas and Sphingobium. A total of eighty bacterial endophytes were characterized in vitro for several plant growth promoting and biocontrol traits including: the phosphate solubilization, the indolic compounds, siderophores, HCN, esterase, lipase, gelatinase and chitinase production. A subset of fifty selected bacteria were tested for their potential as biocontrol agents with in vitro confrontations with the fungal pathogen Fusarium oxysporum as well as the coffee parasitic nematodes Radopholus duriophilus and Pratylenchus coffeae. The three most efficient isolates on F. oxysporum belonging to the Bacillus, Burkholderia, and Streptomyces genera displayed a growth inhibition rate higher than 40%. Finally, five isolates from the Bacillus genus were able to lead to 100% of mortality in 24 h on both R. duriophilus and P. coffeae.
Topics: Antifungal Agents; Antinematodal Agents; Bacteria; Biological Control Agents; Coffea; Coffee; DNA, Ribosomal; Endophytes; Fungi; Fusarium; Phylogeny; Plant Development; Plant Diseases; Plant Roots; RNA, Ribosomal, 16S
PubMed: 33070050
DOI: 10.1016/j.micres.2020.126613 -
Indoor Air Nov 2020Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and...
Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and identified their ecological determinants. We collected vacuum dust from floor and seat surfaces in flight decks and cabins of 18 aircraft, and amplification-free shotgun metagenomics was conducted to characterize the microbial composition. In total, 7437 microbial taxa were identified. The relative abundance for bacteria, eukaryote, viruses, and archaea was 96.9%, 1.8%, 0.3%, and 0.03%, respectively. The top bacterial species mainly derived from outdoor air and human skin included Sphingomonas, Corynebacterium, Micrococcus luteus, Variovorax paradoxus, Paracoccus dentrificans, and Propionibacterium acnes. The abundance of NIAID-defined pathogens was low, accounted for only 0.23% of total microbes. The microbial species and functional composition were structured by the indoor surface type (R = 0.38, Adonis), followed by the manufacturer of the aircraft (R = 0.12) and flight duration (R = 0.07). Indoor surfaces affected species derived from different habitats; the abundance of dry skin and desiccated species was higher on textile surfaces, whereas the abundance of moist and oily skin species was higher on leather surfaces. The growth rates for most microbes were stopped and almost stopped.
Topics: Air Microbiology; Air Pollution, Indoor; Aircraft; Aviation; Comamonadaceae; Dust; Environmental Monitoring; Floors and Floorcoverings; Humans; Metagenomics; Microbiota
PubMed: 32578244
DOI: 10.1111/ina.12707