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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 -
Environmental Science and Pollution... Dec 2023Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF). The...
Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF). The work presented here elaborates on the metabolic pathways involved in the degradation of C1 compounds, many of which are well-known pollutants and toxic to the environment. Investigations on microbial growth and detection of metabolic intermediates corroborate the outcome of the functional genome analysis. Several classes of C1 compounds, such as methanol, methylated amines, aliphatic amides, and naturally occurring quaternary amines like glycine betaine, were tested as growth substrates. The detailed growth and kinetic parameter analyses reveal that P. DMF can efficiently aerobically degrade trimethylamine (TMA) and grow on quaternary amines such as glycine betaine. The results show that the mechanism for halotolerant adaptation in the presence of glycine betaine is dissimilar from those observed for conventional trehalose-mediated halotolerance in heterotrophic bacteria. In addition, a close genomic survey revealed the presence of a Co(I)-based substrate-specific corrinoid methyltransferase operon, referred to as mtgBC. This demethylation system has been associated with glycine betaine catabolism in anaerobic methanogens and is unknown in denitrifying aerobic heterotrophs. This report on an anoxic-specific demethylation system in an aerobic heterotroph is unique. Our finding exposes the metabolic potential for the degradation of a variety of C1 compounds by P. DMF, making it a novel organism of choice for remediating a wide range of possible environmental contaminants.
Topics: Dimethylformamide; Amides; Betaine; Paracoccus; Metabolic Networks and Pathways
PubMed: 38010547
DOI: 10.1007/s11356-023-30858-1 -
Journal of Microbiology and... Jan 2024The study objective was to evaluate the potential production of polyhydroxyalkanoates (PHAs), a biodegradable plastic material, by for which PHA production has never...
The study objective was to evaluate the potential production of polyhydroxyalkanoates (PHAs), a biodegradable plastic material, by for which PHA production has never been reported. To identify the most effective nitrogen-limited culture conditions for PHAs production from this bacterium, batch fermentation using glucose concentrations ranging from 4 g l to 20 g l with a fixed ammonium concentration of 0.5 g l was carried out at 30°C and pH 8.0. A glucose supplement of 12 g l produced the highest PHA concentration (1.6 g l) and PHA content (0.63 g g) thereby identifying the optimal condition for PHA production from this bacterium. Gas chromatography-mass spectrometry analysis suggests that mostly produced copolymer types of poly(3-hydroxybutyrate--3-hydroxyvalerate) [P(3HB--3HV)] from glucose concentrations at 12 g l or higher under the nitrogen-limited conditions. When several other single carbon sources were evaluated for the most efficient PHA production, fructose provided the highest biomass (2.8 g l), and PHAs (1.29 g l) concentrations. Results indicated that this bacterium mostly produced the copolymers P(3HB--3HV) from single carbon sources composing a range of 93-98% of 3-hydroxybutyrate and 2-7% of 3-hydroxyvalerate, whereas mannose-supplemented conditions produced the only homopolymer type of P(3HB). However, when propionic acid as a secondary carbon source were supplemented into the media, produced the copolymer P(3HB--3HV), composed of a 50% maximum monomeric unit of 3-hydroxyvaleric acid (3HV). However, as the concentration of propionic acid increased, cell biomass and PHAs concentrations substantially decreased due to cell toxicity.
Topics: Polyesters; Carbon; Hydroxybutyrates; Polyhydroxyalkanoates; Glucose; Nitrogen; Polyhydroxybutyrates; Paracoccus; Pentanoic Acids; Propionates
PubMed: 37997264
DOI: 10.4014/jmb.2305.05025 -
The Science of the Total Environment Jan 2024The abundant Fe (hydr-) oxides present in wetland sediments can form stable iron (Fe)-organic carbon (OC) complexes (Fe-OC), which are key mechanisms contributing to the...
The abundant Fe (hydr-) oxides present in wetland sediments can form stable iron (Fe)-organic carbon (OC) complexes (Fe-OC), which are key mechanisms contributing to the stability of sedimentary OC stocks in coastal wetland ecosystems. However, the effects of increased flooding and salinity stress, resulting from global change, on the Fe-OC complexes in sediments remain unclear. In this study, we conducted controlled experiments in a climate chamber to quantify the impacts of flooding and salinity on the different forms of Fe (hydr-) oxides binding to OC in the rhizosphere sediments of S. mariqueter as well as the influence on Fe redox cycling bacteria in the rhizosphere. The results of this study demonstrated that prolonged flooding and high salinity treatments significantly reduced the content of organo-metal complexes (Fe) in the rhizosphere. Under high salinity conditions, the content of Fe-OC increased significantly, while flooding led to a decrease in Fe-OC content, inhibiting co-precipitation processes. The association of amorphous Fe (hydr-) oxides (Fe) with OC showed no significant differences under different flooding and salinity treatments. Prolonged flooding significantly increased the relative abundance of Fe-reducing bacteria (FeRB) Deferrisoma and Geothermobacter and decreased polyphenol oxidase in the rhizosphere, while the relative abundance of Fe-oxidizing bacteria (FeOB) Paracoccus and Pseudomonas decreased with increasing salinity and duration of flooding. Overall, short-term water and salinity stress promoted the binding of Fe to OC in the rhizosphere of S. mariqueter, leading to a reduction in the OC content held by Fe. However, there were no significant differences observed in the OC stocks or the total Fe-OC content in the rhizosphere sediments. The findings suggest a degree of consistency in the Fe-OC of the "plant-soil" complex system within tidal flat wetlands, showing resilience to abrupt shifts in flooding and salinity over short periods.
Topics: Oxides; Ecosystem; Rhizosphere; Carbon; Salinity; Iron; Wetlands; Soil
PubMed: 37956840
DOI: 10.1016/j.scitotenv.2023.168447 -
Bioresource Technology Feb 2024Heterotrophic nitrification-aerobic denitrification (HN-AD) shows innovation potential of wastewater treatment process in a single tank. However, how to enrich HN-AD...
Feast/famine ratio regulates the succession of heterotrophic nitrification-aerobic denitrification and autotrophic ammonia oxidizing bacteria in halophilic aerobic granular sludge treating saline wastewater.
Heterotrophic nitrification-aerobic denitrification (HN-AD) shows innovation potential of wastewater treatment process in a single tank. However, how to enrich HN-AD bacteria in activated sludge to enhance their contribution remained unknown. This study explored the impact of the feast/famine (F/F) ratio on the succession of autotrophic ammonia oxidizing bacteria (AOB) and HN-AD bacteria in a halophilic aerobic granular sludge (HAGS) system. As the F/F ratio decreased from 1/9 to 1/15, the total inorganic nitrogen (TIN) removal performance significantly decreased. The proportion of heterotrophic bacteria was dropped from 79.0 % to 33 %. Accordingly, the relative abundance of Paracoccus decreased from 70.8 % to 25.4 %, and the copy number of the napA gene was reduced from 2.2 × 10 copies/g HAGS to 8.1 × 10 copies/g HAGS. It found the F/F ratio regulated the population succession of autotrophic AOB and HN-AD bacteria, thereby providing a solution to achieve the enrichment of HN-AD bacteria in HAGS.
Topics: Nitrification; Wastewater; Sewage; Denitrification; Ammonia; Bioreactors; Heterotrophic Processes; Bacteria; Nitrogen; Betaproteobacteria; Oxidation-Reduction; Aerobiosis
PubMed: 37951552
DOI: 10.1016/j.biortech.2023.129995 -
Environmental Science and Pollution... Dec 2023Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic...
Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms.
Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.
Topics: Denitrification; Nitrification; Bacteria; Biofilms; Carbon; Nitrogen; Soil Microbiology
PubMed: 37945964
DOI: 10.1007/s11356-023-30818-9 -
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 -
Microbiome Oct 2023Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported...
BACKGROUND
Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced by BFS is highly associated with shrimp disease resistance, the causal relationship remains unknown. Here, the promotive roles of gut bacterial community induced by BFS in pathogenic Vibrio infection resistance and its potential micro-ecological and physiological mechanisms were investigated by gut bacterial consortium transplantation and synthetic community (SynCom) construction.
RESULTS
The BFS induced a more stable and resistant gut bacterial community, and significantly enriched some beneficial bacterial taxa, such as Paracoccus, Ruegeria, Microbacterium, Demequina, and Tenacibaculum. Transplantation of a gut bacterial consortium from BFS shrimp (Enrich) greatly enhanced the stability of the bacterial community and resistance against pathogenic V. parahaemolyticus infection in WES shrimp, while transplantation of a gut bacterial consortium from WES shrimp significantly disrupted the bacterial community and increased pathogen susceptibility in both WES and BFS shrimp. The addition of Enrich in shrimp postlarvae also improved the pathogen resistance through increasing the relative abundances of beneficial bacterial taxa and stability of bacterial community. The corresponding strains of five beneficial bacterial taxa enriched in BFS shrimp were isolated to construct a SynCom. The addition of SynCom could not only suppress disease development, but also improve shrimp growth, boost the digestive and immune activities, and restore health in diseased shrimp. Furthermore, the strains of SynCom well colonized shrimp gut to maintain a high stability of bacterial community.
CONCLUSIONS
Our study reveals an important role for native microbiota in protecting shrimp from bacterial pathogens and provides a micro-ecological regulation strategy towards the development of probiotics to ameliorate aquatic animal diseases. Video Abstract.
Topics: Animals; Vibrio parahaemolyticus; Gastrointestinal Microbiome; Penaeidae; Bacteria; Vibrio Infections; Aquaculture
PubMed: 37858205
DOI: 10.1186/s40168-023-01663-2 -
Journal of Environmental Management Dec 2023Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river...
Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river sediments. Until now, little is known about how element coupling processes alter nitrogen metabolism by the microbial functional communities. The primary objective of this research was to clarify the contributory role of microbial-mediated coupled processes in controlling denitrification. Specifically, the study sought to identify the key bioindicators (or metabolic pathway) for preferably regulating and predicting potential denitrification rate (PDR). Here, a total of 40 sediment samples were collected from the inflow rivers of Chaohu Lake under nitrogen stress. The results revealed the ecological importance of methanogens and sulfate reducing bacteria in the microbial interaction network. Correlations between quantitative or predicted genes showed that the methanogenic gene (mcrA) was synergistic with denitrifying genes, further unraveling that the key role of methanogenesis in denitrification process for facilitating nitrogen removal. The PDR of sediments ranged from 0.03 to 133.21 μg N·g·h. The study uncovered specific environmental factors (NH and OM) and microbial indicators (nosZ, mcrA, Paracoccus, Thauera, Methanobrevibacter and Desulfomicrobium) as potential contributors to the variations in PDR. Structural Equation Model (SEM) analysis revealed a significant direct effect of NH on PDR, evidenced by a standardized coefficient (λ) of 0.77 (P < 0.001). Additionally, the findings also emphasized the salient role of methanogens (Methanobrevibacter) and methanogenic gene (mcrA) in indicating PDR. The research's aforementioned findings shed light on the substantial consequences of methanogenesis on nitrogen metabolism in coupled processes, enabling improved control of nitrogen pollution in river sediments. This study provided fresh perspectives on the effects of multiple functional taxa on denitrification, and reinforces the significance of coupling processes for nitrogen removal.
Topics: Denitrification; Rivers; Lakes; Nitrogen; Geologic Sediments
PubMed: 37839205
DOI: 10.1016/j.jenvman.2023.119320