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PloS One 2023The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is...
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
Topics: Paracoccus; DNA Transposable Elements; Genomics; Genomic Islands; Phylogeny; Genome, Bacterial
PubMed: 38117845
DOI: 10.1371/journal.pone.0287947 -
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 -
Journal of Environmental Management Feb 2024It is well accepted that tidal wetland vegetation performs a significant amount of water filtration for wetlands. However, there is currently little information on how...
It is well accepted that tidal wetland vegetation performs a significant amount of water filtration for wetlands. However, there is currently little information on how various wetland plants remove nitrogen (N) and phosphorus (P) and how they differ in their denitrification processes. This study compared and investigated the denitrification and phosphorus removal effects of three typical wetland plants in the Yangtze River estuary wetland (Phragmites australis, Spartina alterniflora, and Scirpus mariqueter), as well as their relevant mechanisms, using an experimental laboratory-scale horizontal subsurface flow constructed wetland (CW). The results showed that all treatment groups with plants significantly reduced N pollutants as compared to the control group without plants. In comparison to S. mariqueter (77.2-83.2%), S. alterniflora and P. australis had a similar total nitrogen (TN)removal effectiveness of nearly 95%. With a removal effectiveness of over 99% for ammonium nitrogen (NH-N), P. australis outperformed S. alterniflora (95.6-96.8%) and S. mariqueter (94.6-96.5%). The removal of nitrite nitrogen (NO-N)and nitrate nitrogen (NO-N)from wastewater was significantly enhanced by S. alterniflora compared to the other treatment groups. Across all treatment groups, the removal rate of PO-P was greater than 95%. P. australis and S. alterniflora considerably enriched more N than S. mariqueter, according to the results of the N isotope labeling experiment. While the rhizosphere and bulk sediments of S. alterniflora were enriched with more simultaneous desulfurization-denitrification bacterial genera (such as Paracoccus, Sulfurovum, and Sulfurimonas), which have denitrification functions, the rhizosphere and bulk sediments of P. australis were enriched with more ammonia-oxidizing archaea and ammonia-oxidizing bacteria. As a result, compared to the other plants, P. australis and S. alterniflora demonstrate substantially more significant ability to remove NH-N and NO-N/NO-N from simulated domestic wastewater.
Topics: Wetlands; Nitrogen; Phosphorus; Ammonia; Nitrogen Dioxide; Wastewater; Plants; Poaceae; China
PubMed: 38109823
DOI: 10.1016/j.jenvman.2023.119864 -
Bioresource Technology Feb 2024The production of polyhydroxyalkanoate (PHA) by mixed microbial culture (MMC) can reduce the pollution of plastics. Ecophysiological study of the microbial community...
Ecological succession and community assembly of mixed microbial culture polyhydroxyalkanoate production systems: Drivers of polyhydroxyalkanoate synthesis and Bdellovibrio predation.
The production of polyhydroxyalkanoate (PHA) by mixed microbial culture (MMC) can reduce the pollution of plastics. Ecophysiological study of the microbial community assembly and succession is helpful for comprehensive understanding the MMC PHA production process. The operation mode of sequential aerobic dynamic discharge - aerobic dynamic feeding (ADD-ADF) was applied and the operation can be divided into acclimation phase and maturation phase. Deterministic process caused by selective pressure dominated the community assembly throughout the operation. In the acclimation phase, the physical selective pressure recovered the settling capacity of the system, and settling ability of the MMC was closely related to function of PHA synthesis. However, in the maturation phase, stochastic process caused sludge bulking, making the settling ability and PHA synthesis function of the MMC independent on each other. Stochastic process led to the succession of the dominant PHA-producing bacteria, for example, the predation of Paracoccus and Thauera by Bdellovibrio.
Topics: Animals; Bioreactors; Polyhydroxyalkanoates; Bdellovibrio; Predatory Behavior; Fermentation; Sewage
PubMed: 38104663
DOI: 10.1016/j.biortech.2023.130204 -
Bioresource Technology Feb 2024L-theanine is a natural non-protein amino acid with wide applications. Thus, a high yield of L-theanine production is required on an industrial scale. Herein, an...
L-theanine is a natural non-protein amino acid with wide applications. Thus, a high yield of L-theanine production is required on an industrial scale. Herein, an efficient L-theanine-producing strain of Corynebacterium glutamicum was constructed by combining protein and metabolic engineering. Firstly, a γ-glutamylmethylamide synthetase from Paracoccus aminovorans (PaGMAS) was isolated and engineered by computer-aided design, the resulting mutant E179K/N105R improved L-theanine yield by 36.61 %. Subsequently, to increase carbon flux towards L-theanine production, the gene ggt which degrades L-theanine, the gene alaT which participated in L-alanine synthesis, and the gene NCgl1221 which encodes glutamate-exporting protein were deleted. Finally, ppk gene was overexpressed to enhance intracellular ATP production. The reprogramed strain produced 44.12 g/L L-theanine with a yield of 57.11 % and productivity of 1.16 g/L/h, which is the highest L-theanine titer reported by Corynebacterium glutamicum. This study provides an efficient and economical biosynthetic pathway for the industrial production of L-theanine.
Topics: Corynebacterium glutamicum; Metabolic Engineering; Fermentation; Glutamic Acid; Glutamates
PubMed: 38103752
DOI: 10.1016/j.biortech.2023.130200 -
Water Science and Technology : a... Dec 2023To investigate energy-saving approaches in wastewater treatment plants and decrease aeration energy consumption, this study successfully established a floc-granule...
To investigate energy-saving approaches in wastewater treatment plants and decrease aeration energy consumption, this study successfully established a floc-granule coexistence system in a sequencing batch airlift reactor (SBAR) employing micro-bubble aeration. The analysis focused on granule formation and pollutant removal under various aeration intensities, and compared its performance with a traditional floc-based coarse-bubble aeration system. The results showed that granulation efficiency was positively associated with aeration intensity, which enhanced the secretion of extracellular polymeric substances (EPSs) and facilitated granule formation. The SBAR with the micro-aeration intensity of 30 mL·min showed the best granulation performance (granulation efficiency 52.6%). In contrast to the floc-based system, the floc-granule coexistence system showed better treatment performance, and the best removal efficiencies of NH-N, TN, and TP were 100.0, 77.0, and 89.5%, respectively. The floc-granule coexistence system also enriched higher abundance of nutrients removal microbial species, such as Nitrosomonas (0.05-0.14%), Nitrospira (0.14-2.32%), Azoarcus (2.95-12.17%), Thauera (0.43-1.95%), and Paracoccus (0.76-2.89%). The energy-saving potential was evaluated, which indicated it is feasible for the micro-aeration floc-granule coexistence system to decrease the aeration consumption by 14.4% as well as improve the effluent.
Topics: Sewage; Waste Disposal, Fluid; Bioreactors; Bacteria; Aerobiosis; Nitrogen
PubMed: 38096087
DOI: 10.2166/wst.2023.376 -
Aquatic Toxicology (Amsterdam,... Dec 2023The red swamp crayfish (Procambarus clarkii) is an important farming species in China and there is a high degree of overlap between the main crayfish production areas...
The red swamp crayfish (Procambarus clarkii) is an important farming species in China and there is a high degree of overlap between the main crayfish production areas and areas contaminated with the heavy metal lead (Pb), thus putting crayfish farming at potential risk of Pb contamination. To assess the toxic effects of Pb on crayfish, in this study they were exposed to different concentrations of Pb (0, 0.1, 1, 10, 50 mg/L) for 72 h, and 0.1 mg/L represents the level of Pb in the contaminated water. Histomorphology and activities of antioxidant or immune-related enzymes suggest that the damage of Pb to the hepatopancreas and intestine was dose- and time-dependent, with the intestine being more sensitive to Pb than the hepatopancreas. Notably, after a short period (24 h) of stress at low concentrations (0.1 mg/L) of Pb, the malondialdehyde (MDA) content and antioxidant enzymes such as catalase (CAT) and glutathione peroxidase (GSH-Px) in the intestine of crayfish showed significant changes, indicating that low concentrations of Pb were also highly detrimental to crayfish. High-throughput sequencing of the intestinal microbial community indicated that Pb exposure led to a disturbance in the relative abundance of intestinal bacteria, increasing the abundance of pathogenic bacteria (Bosea, Cloacibacterium, Legionella spp.) and decreasing the abundance of potentially beneficial bacteria (Chitinibacter, Chitinilyticum, Paracoccus, Microbacterium, Demequina, and Acinetobacter spp.). In conclusion, Pb damages the hepatopancreas and intestinal barrier of crayfish, leading to the destruction of their anti-stress ability and immune response, and at the same time disrupts the homeostasis of intestinal microbes, resulting in adverse effects on the gut. This study contributed to the assessment of the ecotoxicity of the heavy metal Pb to the crustacean aquatic animals.
Topics: Animals; Antioxidants; Astacoidea; Gastrointestinal Microbiome; Lead; Water Pollutants, Chemical; Metals, Heavy; Fresh Water
PubMed: 38041968
DOI: 10.1016/j.aquatox.2023.106768 -
Environmental Microbiology Reports Feb 2024Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this...
Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.
Topics: Humans; Nitric Oxide; Denitrification; Nitrites; Nitrous Oxide; Nitrogen
PubMed: 38037543
DOI: 10.1111/1758-2229.13221 -
Environmental Research Feb 2024Aerobic granular sludge (AGS) needs a long start-up time and always shows unstable performance when it is used to treat low-strength wastewater. In this study, a rapid...
Aerobic granular sludge (AGS) needs a long start-up time and always shows unstable performance when it is used to treat low-strength wastewater. In this study, a rapid static feeding combined with Fe addition as a novel strategy was employed to improve the formation and stability of AGS in treating low-strength wastewater. Fe-AGS was formed within only 7 days and showed favorable pollutant removal capability and settling performance. The ammonia nitrogen (NH-N) and chemical oxygen demand (COD) concentration in the effluent were lower than 5 mg/L and 50 mg/L after day 23, respectively. The sludge volume index (SVI) and mixed liquid suspended solids (MLSS) was 37 mL/g and 2.15 g/L on day 50, respectively. Rapid static feeding can accelerate granules formation by promoting the growth of heterotrophic bacteria, but the granules are unstable due to filamentous bacteria overgrowth. Fe addition can inhibit the growth of filamentous bacteria and promote the aggregation of functional bacteria (eg. Nitrosomonas, Nitrolancea, Paracoccus, Diaphorobacter) by enhancing the secretion of extracellular polymeric substances (EPS). This study provides a new way for AGS application in low-strength wastewater treatment.
Topics: Wastewater; Sewage; Waste Disposal, Fluid; Aerobiosis; Bioreactors; Nitrogen
PubMed: 38029821
DOI: 10.1016/j.envres.2023.117770 -
Archives of Microbiology Nov 2023Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation...
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
Topics: Paracoccus; Dimethylformamide; Bacteria; Genomics; Water
PubMed: 38015256
DOI: 10.1007/s00203-023-03729-z