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Frontiers in Microbiology 2024Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut...
Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut microbe composition is crucial to help mitigate potential threats posed to wild populations. However, gut microbiological trait similarities between wild and artificially bred green turtles remain unexplored. Therefore, this study compared the gut microbiological characteristics of wild and artificially bred green turtles () through high-throughput Illumina sequencing technology. The α-diversity of intestinal bacteria in wild green turtles, as determined by Shannon and Chao indices, significantly surpasses that of artificial breeding green turtles ( < 0.01). However, no significant differences were detected in the fungal α-diversity between wild and artificially bred green turtles. Meanwhile, the β-diversity analysis revealed significant differences between wild and artificially bred green turtles in bacterial and fungal compositions. The community of gut bacteria in artificially bred green turtles had a significantly higher abundance of Fusobacteriota including those belonging to the , , and genera than that of the wild green turtle. In contrast, the abundance of bacteria belonging to the phylum Actinobacteriota and genus significantly decreased. Regarding the fungal community, artificially bred green turtles had a significantly higher abundance of , , and and a lower abundance of and than the wild green turtle. The PICRUSt2 analyses demonstrated significant differences in the functions of the gut bacterial flora between groups, particularly in carbohydrate and energy metabolism. Fungal functional guild analysis further revealed that the functions of the intestinal fungal flora of wild and artificially bred green turtles differed significantly in terms of animal pathogens-endophytes-lichen parasites-plant pathogens-soil saprotrophs-wood saprotrophs. BugBase analysis revealed significant potential pathogenicity and stress tolerance variations between wild and artificially bred green turtles. Collectively, this study elucidates the distinctive characteristics of gut microbiota in wild and artificially bred green turtles while evaluating their health status. These findings offer valuable scientific insights for releasing artificially bred green turtles and other artificially bred wildlife into natural habitats.
PubMed: 38873159
DOI: 10.3389/fmicb.2024.1412015 -
Applied Microbiology and Biotechnology Jun 2024Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene... (Review)
Review
Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. KEY POINTS: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways.
Topics: Ethylene Glycol; Metabolic Engineering; Metabolic Networks and Pathways; Bacteria; Pseudomonas putida; Biofuels; Escherichia coli
PubMed: 38861200
DOI: 10.1007/s00253-024-13179-2 -
Water Research Aug 2024Overuse of antibiotics has led to their existence in nitrogen-containing water. The impacts of antibiotics on bio-denitrification and the metabolic response of...
Overuse of antibiotics has led to their existence in nitrogen-containing water. The impacts of antibiotics on bio-denitrification and the metabolic response of denitrifiers to antibiotics are unclear. We systematically analyzed the effect of ciprofloxacin (CIP) on bio-denitrification and found that 5 mg/L CIP greatly inhibited denitrification with a model denitrifier (Paracoccus denitrificans). Nitrate reduction decreased by 32.89 % and nitrous oxide emission increased by 75.53 %. The balance analysis of carbon and nitrogen metabolism during denitrification showed that CIP exposure blocked electron transfer and reduced the flow of substrate metabolism used for denitrification. Proteomics results showed that CIP exposure induced denitrifiers to use the pentose phosphate pathway more for substrate metabolism. This caused a substrate preference to generate NADPH to prevent cellular damage rather than NADH for denitrification. Notably, despite denitrifiers having antioxidant defenses, they could not completely prevent oxidative damage caused by CIP exposure. The effect of CIP exposure on denitrifiers after removal of extracellular polymeric substances (EPS) demonstrated that EPS around denitrifiers formed a barrier against CIP. Fluorescence and infrared spectroscopy revealed that the binding effect of proteins in EPS to CIP prevented damage. This study shows that denitrifiers resist antibiotic stress through different intracellular and extracellular defense strategies.
Topics: Ciprofloxacin; Denitrification; Anti-Bacterial Agents; Paracoccus denitrificans
PubMed: 38851110
DOI: 10.1016/j.watres.2024.121851 -
Bioresource Technology Jul 2024The efficient degradation of antibiotics holds significant implications for mitigating environmental pollution. This study synthesized a montmorillonite chitosan...
The efficient degradation of antibiotics holds significant implications for mitigating environmental pollution. This study synthesized a montmorillonite chitosan composite material (MMT-CS) using the gel template method. Subsequently, a bio-enhanced reactor was constructed to facilitate the degradation of chlorotetracycline (CTC). The addition of MMT-CS composite material enables the degradation of different concentrations of CTC. MMT-CS, a conductive carrier, effectively promotes microbial adhesion and boosts the metabolic activity of functional microorganisms. Additionally, it facilitates the maintenance of microbial activity under CTC pressure by promoting the secretion of extracellular polymeric substances, increasing critical enzyme activity, and enhancing the electron transfer capacity within the system. In this MMT-CS bio-enhanced process, Paracoccus (11.4%) and Bacillus (3.9%) are utilized as essential bacteria genes. The results of metabolic pathways prediction indicated significant enhancements in membrane-transport, nucleotide-metabolism, replication-repair, and lipid-metabolism. Thus, the developed self-supporting MMT-CS bio-enhanced process ensured the stability of the system during the removal of antibiotics.
Topics: Bentonite; Chlortetracycline; Biodegradation, Environmental; Electron Transport; Chitosan; Anti-Bacterial Agents; Bioreactors
PubMed: 38838830
DOI: 10.1016/j.biortech.2024.130928 -
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 -
Scientific Reports Jun 2024We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in...
We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, housing structure, and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs. 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from Mexican homes was enriched with Alishewanella, Paracoccus, Rheinheimera genera and Intrasporangiaceae family. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.
Topics: Dust; Arizona; Humans; Mexico; Housing; Asthma; Bacteria; Female; Family Characteristics; Male; Metagenomics
PubMed: 38834753
DOI: 10.1038/s41598-024-63356-6 -
Frontiers in Microbiology 2024Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is...
Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (, and ). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.
PubMed: 38800754
DOI: 10.3389/fmicb.2024.1388973 -
Antonie Van Leeuwenhoek May 2024A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei...
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6 belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2 with 98.1% similarity, Paracoccus fontiphilus MVW-1 (97.9%), Paracoccus everestensis S8-55 (97.7%), Paracoccus subflavus GY0581 (97.6%), Paracoccus sediminis CMB17 (97.3%), Paracoccus caeni MJ17 (97.0%), and Paracoccus angustae E6 (97.0%). The genome size of strain EF6 was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6 and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C ω6c and/or C ω7c) and C (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6 displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6 possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6 a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6 is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6 (= GDMCC 1.3400 = JCM 35642 = MCCC 1K08702).
Topics: Wetlands; Phylogeny; Paracoccus; RNA, Ribosomal, 16S; Fatty Acids; Base Composition; DNA, Bacterial; China; Sodium Selenite; Bacterial Typing Techniques; Phospholipids; Sequence Analysis, DNA; Nucleic Acid Hybridization; Oxidation-Reduction; Drug Resistance, Bacterial
PubMed: 38777900
DOI: 10.1007/s10482-024-01969-7 -
Bioresource Technology Jul 2024In this study, the possibility of an auto-aggregating bacterium Pseudomonas strain XL-2 with heterotrophic nitrification-aerobic denitrification capacity for improving...
Evaluation of aerobic granulation performance bioaugmented with the auto-aggregating bacterium Pseudomonas stutzeri strain XL-2 with heterotrophic nitrification-aerobic denitrification capacity.
In this study, the possibility of an auto-aggregating bacterium Pseudomonas strain XL-2 with heterotrophic nitrification-aerobic denitrification capacity for improving granulation and nitrogen removal was evaluated. The results showed that the supplementation of strain XL-2 promoted granulation, making R1 (experimental group with strain XL-2) dominated by granules at 14 d, which was 12 days earlier than R2 (control group without strain XL-2). This was attributed to the promotion of extracellular polymeric substances (EPS) secretion, particularly proteins by adding strain XL-2, thereby improving the hydrophobicity of sludge and altering the proteins secondary structures to facilitate aggregation. Meanwhile, adding strain XL-2 improved simultaneous nitrification and denitrification efficiency of R1. Microbial community analysis indicated that strain XL-2 successfully proliferated in aerobic granule sludge and might induce the enrichment of genera such as Flavobacterium and Paracoccus that were favorable for EPS secretion and denitrification, jointly promoting granulation and enhancing nitrogen removal efficiency.
Topics: Denitrification; Nitrification; Pseudomonas stutzeri; Aerobiosis; Sewage; Nitrogen; Heterotrophic Processes; Extracellular Polymeric Substance Matrix; Bioreactors
PubMed: 38777236
DOI: 10.1016/j.biortech.2024.130869 -
Environmental Research Aug 2024In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results...
In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results presented the salinity except for 5% imposed negligible effects on aniline degradation performance. Nitrification had prominent resistance to salinity (0%-1.5%) while were significantly restrained when salinity increased. The total nitrogen (TN) removal efficiency of Z4 (1.5%) was 20.5% higher than Z1 (0%) during the stable operation phase. Moreover, high throughput sequencing analysis showed that halophilic bacterium, such as Halomonas, Rhodococcus, remained greater survival advantages in high salinity system. The substantial enrichment of Flavobacterium, Dokdonella, Paracoccus observed in Z4 ensured its excellent nitrogen removal performance. The close cooperation among dominant functional bacteria was strengthened when salt content was below 1.5% while exceeding 1.5% led to the collapse of metabolic capacity through integrating the toxicity of aniline and high osmotic pressure.
Topics: Aniline Compounds; Biodegradation, Environmental; Water Pollutants, Chemical; Salt Stress; Bacteria; Bioreactors; Salinity
PubMed: 38762003
DOI: 10.1016/j.envres.2024.119162