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Current Genetics Jun 2017One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the...
One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.
Topics: Animals; Anthozoa; Brazil; DNA, Bacterial; Ecosystem; Genome, Bacterial; Paracoccus; Phylogeny; Symbiosis
PubMed: 27796486
DOI: 10.1007/s00294-016-0658-3 -
Antonie Van Leeuwenhoek Aug 2023A novel moderately halophilic bacterial strain, designated Z330, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China...
A novel moderately halophilic bacterial strain, designated Z330, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330 exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803 (97.6%), Paracoccus seriniphilus NBRC 100798 (97.6%) and Paracoccus aestuarii DSM 19484 (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330 was most closely related to P. seriniphilus NBRC 100798 and P. fistulariae KCTC 22803. Strain Z330 grew optimally at 28-30 °C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330 occurred at 0.5-16% NaCl, indicated strain Z330 was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330 was identified as ubiquinone-10. The major polar lipids of strain Z330 were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330 was summed feature 8 (C ω6c and/or C ω7c). The draft genome sequence of strain Z330 includes 4,084,570 bp in total (N50 = 174,985 bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330 was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803, Paracoccus seriniphilus NBRC 100798, Paracoccus aestuarii DSM 19484 and Paracoccus denitrificans 1A10901, respectively. And the average nucleotide identity (ANIb) values between strain Z330 and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330 (= KCTC 92727 = MCCC 1K08325).
Topics: Animals; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sodium Chloride; DNA, Bacterial; Paracoccus; Fatty Acids; Invertebrates; China; Sequence Analysis, DNA; Bacterial Typing Techniques
PubMed: 37231142
DOI: 10.1007/s10482-023-01848-7 -
Bioresource Technology Feb 2023Astaxanthin (AXT) is a ketocarotenoid with several properties, including antioxidant, antidiabetic and anticancer with a wide range of applications in cosmeceutical,... (Review)
Review
Astaxanthin (AXT) is a ketocarotenoid with several properties, including antioxidant, antidiabetic and anticancer with a wide range of applications in cosmeceutical, feed, food and pharmaceuticals sectors. The large fraction of AXT available in the market is obtained by chemical route, but the consumers preference for natural products are changing the global market of AXT, and due to that several companies are looking for potential alternative sources such as Gram-negative bacteria Paracoccus carotinifaciens (P. carotinifaciens) to obtain natural AXT. The aim of this critical review is to provide a comprehensive overview of the latest AXT research findings and characteristics of the hyperproducer-AXT P. carotinifaciens. Moreover, a brief description of the potential application of P. carotinifaciens for the production of natural AXT at industrial scale for commercial purposes and the latest advancements in the upstream and downstream procedures following the biorefinery and circular economy percepts are considered.
Topics: Xanthophylls; Antioxidants; Paracoccus
PubMed: 36535613
DOI: 10.1016/j.biortech.2022.128499 -
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 -
Chemosphere Dec 2022In order to reduce the resource and energy consumption of traditional biological nitrogen removal (BNR) process, heterotrophic nitrification-aerobic denitrification...
In order to reduce the resource and energy consumption of traditional biological nitrogen removal (BNR) process, heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria was in situ enriched in membrane aerated biofilm reactor (MABR) by inoculating conventional activated sludge. Contaminants removal performance, EPS composition and microbial community were explored. The results indicated that the average removal efficiency of COD and TN under optimal condition reached 84.13% and 91.54%, respectively, which demonstrated that the reactor possessed excellent contaminants removal capacity. EPS analysis suggested that abundant protein especially tryptophan protein-like substance played a vital role in maintaining the microbial stability of biofilms. Multiple HN-AD genera, mainly Paracoccus, were detected with the highest relative abundance of 54.70%, which confirmed the successful enrichment of the HN-AD bacteria. Conventional nitrifiers and denitrifiers also thrived in biofilm, which demonstrated the synergistic nitrogen removal of multiple microorganisms. This study provided important insights into application of HN-AD bacteria and synergistic nitrogen removal in BNR system.
Topics: Nitrification; Denitrification; Heterotrophic Processes; Sewage; Tryptophan; Bioreactors; Biofilms; Nitrogen; Bacteria; Wastewater
PubMed: 36181858
DOI: 10.1016/j.chemosphere.2022.136643 -
The Science of the Total Environment Mar 2019This work demonstrates bacterial oxidation of mercury (Hg) coupled to nitric oxide (NO) reduction in a denitrifying membrane biofilm reactor (MBfR). In 93 days'...
This work demonstrates bacterial oxidation of mercury (Hg) coupled to nitric oxide (NO) reduction in a denitrifying membrane biofilm reactor (MBfR). In 93 days' operation, Hg and NO removal efficiency attained 90.7% and 74.1%, respectively. Thauera, Pseudomonas, Paracoccus and Pannonibacter played dual roles as Hg oxidizers and denitrifiers simultaneously. Denitrifying bacteria and the potential mercury resistant bacteria dominated the bacterial community. Denitrification-related genes (norB, norC, norD, norE, norQ and norV) and enzymatic Hg oxidation-related genes (katG, katE) were responsible for bacterial oxidation of Hg and NO reduction, as shown by metagenomic sequencing. XPS, HPLC-ICP-MS and SEM-EDS indicated the formation of a stable mercuric species (Hg) reasulting from Hg oxidation in the biofilm. Bacterial oxidation of Hg was coupled to NO reduction in which Hg served as the initial electron donor while NO served as the terminal electron acceptor and thereby redox between Hg and NO was formed. MBfR was capable of both Hg bio-oxidation and denitrifying NO reduction. This research opens up new possibilities for application of MBfR to simultaneous flue gas demercuration and denitration.
Topics: Bacteria; Bacterial Physiological Phenomena; Biofilms; Bioreactors; DNA, Bacterial; Denitrification; Membranes, Artificial; Mercury; Metagenome; Nitric Oxide; Oxidation-Reduction; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 30678005
DOI: 10.1016/j.scitotenv.2018.12.105 -
IUBMB Life Dec 2018There are many similarities between the oxidative phosphorylation apparatus of mitochondria and those found in the cytoplasmic membranes of alpha-proteobacteria,... (Review)
Review
There are many similarities between the oxidative phosphorylation apparatus of mitochondria and those found in the cytoplasmic membranes of alpha-proteobacteria, exemplified by Paracocus denitrificans. These similarities are reviewed here alongside consideration of the differences between mitochondrial and bacterial counterparts, as well as the loss from the modern mitochondria of many of the bacterial respiratory proteins. The assembly of c-type cytochromes is of particular evolutionary interest as the post-translational apparatus used in the alpha-proteobacteria is found in plants, and for example in eukyarotic species including algae of various kinds together with jakobids, but has been superseded by different systems in mitochondria of metazoans and trypanosomatids. All mitochondrial cytochromes c have the N-terminal sequence feature that is recognised by the metazoan system whereas the bacterial counterparts do not, suggesting that the loss of the bacterial system from eukaryotes occurred in the context of an already present recognition sequence in the eukaryotic cytochromes. Interestingly, in the case of cytochromes c the putative recognition features for the metazoans appear to be substantially present in the bacterial proteins. The ability to prepare from P. denitrificans inverted membrane vesicles with classic respiratory control presents a valuable system from which to draw lessons concerning the long debated topic of what controls the rates of respiration and ATP synthesis in mitochondria. © 2018 IUBMB Life, 70(12):1214-1221, 2018.
Topics: Adenosine Triphosphate; Cell Membrane; Cytochromes c; Electron Transport; Mitochondria; Oxidative Phosphorylation; Paracoccus denitrificans
PubMed: 30428155
DOI: 10.1002/iub.1962 -
Environmental Research Dec 2022This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity...
This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0-30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 10-9.12 × 10 (nitrogen functional genes) and 1.24 × 10-8.43 × 10 copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23-9.23, 400.03-755.91, 3.12-35.24 and 30.51-300.04 nmolN·g·d, respectively. The denitrification process contributed to 73.59-88.65% of NO reduction, compared to 0.71-13.20% and 8.20-15.42% via DNRA and anammox, as 83.83-90.74% of N production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28-99.23% of NH oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.
Topics: Ammonium Compounds; Bacteria; Denitrification; Nitrates; Nitrogen; Oxidation-Reduction; RNA, Ribosomal, 16S; Rhizosphere; Salinity; Soil; Wetlands
PubMed: 36055394
DOI: 10.1016/j.envres.2022.114235 -
International Journal of Systematic and... Sep 2022A bacterial strain, designated S8-55, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level....
A bacterial strain, designated S8-55, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus , and explore the antioxidant capacity of strain S8-55. The polyphasic study confirmed the affiliation of strain S8-55 with the genus . Strain S8-55 was aerobic, Gram-negative and oxidase- and catalase positive. Cells were orange-pigmented, ellipsoid and had no spore formation, no flagella and no motility. Strain S8-55 grow at 10-37 °C, pH 7-11 and without NaCl. Ubiquinone 10 was its predominant respiratory menaquinone. The polar lipids of strain S8-55 were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and three unidentified lipids. Its major fatty acids were summed feature 8 (C 7 and/or C 6). The G+C content was 64.3 mol%. The phylogenetic analysis based on the 16S rRNA sequence showed that strain S8-55 was closely related to E6 (97.9 %), 011410 (97.9 %) and THG-T2.8 (97.8 %). The average nucleotide identity values among strain S8-55 and CCTCC AB 2015056, KCTC 42845 and CCTCC AB 2016181 were 84.1, 84.5 and 76.3 %, respectively. The genome of strain S8-55 contained antioxidant genes such as , , , and . Based on its morphological, physiological and chemical taxonomic characteristics, strain S8-55 (=JCM 35 227=GDMCC 1.3026) should be classified as a novel species of the genus with the proposed name sp. nov.
Topics: Antioxidants; Bacterial Typing Techniques; Base Composition; Cardiolipins; Catalase; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Nucleotides; Paracoccus; Phosphatidylcholines; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sodium Chloride; Vitamin K 2
PubMed: 36129740
DOI: 10.1099/ijsem.0.005562 -
International Journal of Systematic and... Mar 2020The present study aimed to examine the taxonomic relationship between two species, Ghosh . 2006 and (Harrison 1983) Katayama . 1996. Comparison of 16S rRNA gene...
The present study aimed to examine the taxonomic relationship between two species, Ghosh . 2006 and (Harrison 1983) Katayama . 1996. Comparison of 16S rRNA gene sequences revealed that JJJ was highly similar (99.9 %) to A2. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus . Whole genomic comparison between the two strains showed a digital DNA-DNA hybridization estimate of 82. 0 % and an average nucleotide identity value of 98.2 %, clearly indicating that the two strains were members of the same species. Moreover, the type strains of both species shared similar physiological and biochemical properties and fatty acids profiles. Based on genotypic and phenotypic evidence, we conclude that Ghosh . 2006 is a later heterotypic synonym of (Harrison 1983) Katayama . 1996 according to the priority of publication and validation of the name.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Paracoccus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32038007
DOI: 10.1099/ijsem.0.004014