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Environmental Research Nov 2023The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for...
The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.
Topics: Petroleum; Ecosystem; Sewage; Soil Pollutants; Soil Microbiology; RNA, Ribosomal, 16S; Bacteria; Biodegradation, Environmental; Soil; Genetic Variation
PubMed: 37517495
DOI: 10.1016/j.envres.2023.116779 -
Current Microbiology Apr 2024A novel Paracoccus-related strain, designated YLB-12, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The...
A novel Paracoccus-related strain, designated YLB-12, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11 (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588 (97.4%), Paracoccus rhizosphaerae LMG 26205 (97.2%), Paracoccus beibuensis CGMCC 1.7295 (97.1%) and Paracoccus halotolerans CFH 90064 (97.0%). The DNA‒DNA hybridization values between strain YLB-12 and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12 was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12 also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (Cω6c /Cω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12 represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12 (= MCCC 1A17213 = KCTC 82197).
Topics: Phylogeny; RNA, Ribosomal, 16S; Fatty Acids; Paracoccus; DNA
PubMed: 38592513
DOI: 10.1007/s00284-024-03637-5 -
International Journal of Systematic and... Aug 2023Strain designated TK19116 was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China. The bacterium was Gram-stain-negative, aerobic,...
Strain designated TK19116 was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China. The bacterium was Gram-stain-negative, aerobic, oxidase-positive and catalase-positive. Cells of the strain TK19116 were short-rod-shaped and non-motile. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain TK19116 belonged to the genus , with the highest sequence similarity to 4-2 (97.1 %). The average nucleotide identity values between the strain TK19116 with 4-2, J6, M26 and BM15 were 75.3, 76.7, 76.7 and 75.8%, respectively. The digital DNA-DNA hybridization value between the strain TK19116 with 4-2, J6, M26 and BM15 were 19.7, 20.3, 20.5 and 20.0%, respectively. The main respiratory quinone of strain TK19116 was ubiquinone 10. The polar lipids include aminolipid, phosphatidylcholine, diphosphatidylglycerol, glycolipid, phosphatidylglycerol and phospholipid. The principal fatty acid of strain TK19116 was summed feature 8 (C 6 and/or C 7). The G+C content of the chromosomal DNA was 64.2 %. The combination of the results of the phylogenetic, phenotypic and chemotaxonomic analysis, strain TK19116 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TK19116 (= MCCC 1K08025=JCM 35527).
Topics: Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Bacterial Typing Techniques; Sequence Analysis, DNA; Phospholipids; Paracoccus
PubMed: 37535057
DOI: 10.1099/ijsem.0.005998 -
Biotechnology and Bioengineering Mar 2024The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic...
The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.
Topics: Bacteria; Tetrachloroethylene; Lactic Acid; Biodegradation, Environmental; Catechols
PubMed: 38116701
DOI: 10.1002/bit.28630 -
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 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 -
Environmental Research Jan 2024Selenium-containing wastewater has a high concentration of nitrogen compounds (ammonia nitrogen [NH-N]), leading to water pollution. Thus, the simultaneous reduction of...
Selenium-containing wastewater has a high concentration of nitrogen compounds (ammonia nitrogen [NH-N]), leading to water pollution. Thus, the simultaneous reduction of selenium and removal of nitrogen compounds during wastewater treatment has become the top priority. However, the exogenous bacteria that can simultaneously reduce selenite and remove ammonia nitrogen and colonize in the wastewater treatment systems have not been reported. Additionally, the effects and the underlying mechanism of biofortification on the reduction and removal efficiency of the microorganisms remain unclear. In this study, we investigated the simultaneous selenite reduction and nitrogen removal efficiency of Paracoccus sp. (strain SSJ) isolated from selenium-contaminated soil and explored biofortification effects on the composition and structure of the microbial community. Using sequencing biofilm batch reactors (SBBRs), the structural and functional characteristics of the microbial community were systematically compared between the control (group A) and biofortified (group B) groups. Strain SSJ could simultaneously reduce 63.28% of selenite and remove 93.05% of NH-N within 24 h. Moreover, no accumulation of nitrate nitrogen (NO-N) and nitrite nitrogen (NO-N) was observed in the reaction process. The performance and stability of the SBBRs enhanced by strain SSJ were greatly improved. Illumina sequencing results showed that strain SSJ was surprisingly colonized, and Paracoccus was the predominant genus in group B (relative abundance: 13.93%). Moreover, PICRUSt2 analysis results suggested that the microbial community in group B demonstrated increased rates of ammonia nitrogen removal through ammonia assimilation and selenite reduction through sulfur metabolism and glutathione-mediated selenite reduction pathway. In summary, our findings shed light on the mechanism for simultaneous selenite reduction and nitrogen removal by biofortification and provide novel microbial resources for the treatment of selenite-containing wastewater.
Topics: Nitrogen; Paracoccus; Ammonia; Denitrification; Selenium; Wastewater; Nitrogen Compounds; Microbiota; Selenious Acid
PubMed: 37918763
DOI: 10.1016/j.envres.2023.117564 -
Frontiers in Microbiology 2023The microorganisms associated with a plant influence its growth and fitness. These microorganisms accumulate on the aerial and root surfaces of plants, as well as within...
The microorganisms associated with a plant influence its growth and fitness. These microorganisms accumulate on the aerial and root surfaces of plants, as well as within the plants, as endophytes, although how the interaction between microorganisms protects the plant from pathogens is still little understood. In the current study, the impact of assembled the bacterial communities against the pathogenic fungus to promote L. growths was investigated. We established a model of bacterium-fungus-plant system. Eight bacterial strains and a fungal pathogen (Glo) were isolated from wild roots and leaves, respectively. We assembled the six-bacteria community (C6: , sp., sp., sp., sp., and sp.) with inhibition, and eight-bacteria community (C8) composing of C6 plus another two bacteria ( and sp.) without inhibition against Glo in individually dual culture assays. Inoculation of seedlings with C8 significantly reduced impact of Glo. The growth and disease suppression of seedlings inoculated with C8 + Glo were significantly better than those of seedlings inoculated with only Glo. C8 had more inhibitory effects on Glo, and also enhanced the contents of four metabolites in seedling roots compared to Glo treatment only. Additionally, the inhibitory effects of root extracts from seedlings showed that Glo was most sensitive, the degree of eight bacteria sensitivity were various with different concentrations. Our findings suggested that the non-inhibitory bacteria played a vital role in the bacterial community composition and that some bacterial taxa were associated with disease suppression. The construction of a defined assembled bacterial community could be used as a biological fungicide, promoting biological disease control of plants.
PubMed: 37876787
DOI: 10.3389/fmicb.2023.1218474 -
Environmental Microbiology Reports Jun 2024As part of ongoing efforts to discover novel polyhydroxyalkanoate-producing bacterial species, we embarked on characterizing the thermotolerant species, Paracoccus...
As part of ongoing efforts to discover novel polyhydroxyalkanoate-producing bacterial species, we embarked on characterizing the thermotolerant species, Paracoccus kondratievae, for biopolymer synthesis. Using traditional chemical and thermal characterization techniques, we found that P. kondratievae accumulates poly(3-hydroxybutyrate) (PHB), reaching up to 46.8% of the cell's dry weight after a 24-h incubation at 42°C. Although P. kondratievae is phylogenetically related to the prototypical polyhydroxyalkanoate producer, Paracoccus denitrificans, we observed significant differences in the PHB production dynamics between these two Paracoccus species. Notably, P. kondratievae can grow and produce PHB at elevated temperatures ranging from 42 to 47°C. Furthermore, P. kondratievae reaches its peak PHB content during the early stationary growth phase, specifically after 24 h of growth in a flask culture. This is then followed by a decline in the later stages of the stationary growth phase. The depolymerization observed in this growth phase is facilitated by the abundant presence of the PhaZ depolymerase enzyme associated with PHB granules. We observed the highest PHB levels when the cells were cultivated in a medium with glycerol as the sole carbon source and a carbon-to-nitrogen ratio of 10. Finally, we found that PHB production is induced as an osmotic stress response, similar to other polyhydroxyalkanoate-producing species.
Topics: Hydroxybutyrates; Polyesters; Paracoccus; Hot Temperature; Temperature; Phylogeny; Polyhydroxybutyrates
PubMed: 38838099
DOI: 10.1111/1758-2229.13260 -
Microbiology Spectrum Sep 2023Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the...
Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the environment and human health. Although microbial degradation methods have been widely applied, some issues remain, including low degradation efficiency and poor environmental adaptability. In this regard, constructing efficient degrading bacteria by metabolic engineering is an ideal solution to these challenges. In this study, we used DYTN-1, a superior nitrogen removal environment strain, as chassis to construct an SMX degradation pathway, obtaining a new bacteria for simultaneous degradation of SMX and removal of ammonia nitrogen. In doing this, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. After degradation pathway expression level optimization and FMN reductase optimization, SMX degradation efficiency was significantly improved. The constructed pIAB-P strain exhibited superior co-degradation of SMX and ammonia nitrogen contaminants with degradation rates of 44% and 71%, respectively. This study could pave the way for SMX degradation engineered strain design and evolution of environmental bioremediation. IMPORTANCE The abuse of sulfamethoxazole (SMX) had led to an increased accumulation in the environment, resulting in the disruption of the structure of microbial communities, further disrupting the bio-degradation process of other pollutants, such as ammonia nitrogen. To solve this challenge, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. Then SMX degradation efficiency was significantly improved with degradation pathway expression level optimization and FMN reductase optimization. Finally, the superior nitrogen removal environment strain, DYTN-1, obtained an SMX degradation function. This pioneering study of metabolic engineering to enhance the SMX degradation in microorganisms could pave the way for designing the engineered strains of SMX and nitrogen co-degradation and the environmental bioremediation.
PubMed: 37732744
DOI: 10.1128/spectrum.00146-23