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Current Microbiology Jun 2024Standing dead trees (snags) are recognized for their influence on methane (CH) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude...
Standing dead trees (snags) are recognized for their influence on methane (CH) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH fluxes were highly variable (- 0.11-0.51 mg CH m h). CH production was measured in three out of ten snags; whereas, CH consumption was measured in two out of ten snags. Potential CH production and oxidation in one core from each snag was assayed in vitro. A single core produced CH under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH g h, respectively. Four cores oxidized CH under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH g h. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH cycling in coastal ghost forest wetlands to a shifting coastal landscape.
Topics: Methane; Forests; Microbiota; Wetlands; Bacteria; RNA, Ribosomal, 16S; Trees; Phylogeny; Oxidation-Reduction; Archaea; Aerobiosis
PubMed: 38896154
DOI: 10.1007/s00284-024-03767-w -
International Journal of Molecular... May 2024Time-series experiments are crucial for understanding the transient and dynamic nature of biological phenomena. These experiments, leveraging advanced classification and...
Time-series experiments are crucial for understanding the transient and dynamic nature of biological phenomena. These experiments, leveraging advanced classification and clustering algorithms, allow for a deep dive into the cellular processes. However, while these approaches effectively identify patterns and trends within data, they often need to improve in elucidating the causal mechanisms behind these changes. Building on this foundation, our study introduces a novel algorithm for temporal causal signaling modeling, integrating established knowledge networks with sequential gene expression data to elucidate signal transduction pathways over time. Focusing on s () aerobic to anaerobic transition (AAT), this research marks a significant leap in understanding the organism's metabolic shifts. By applying our algorithm to a comprehensive regulatory network and a time-series microarray dataset, we constructed the cross-time point core signaling and regulatory processes of 's AAT. Through gene expression analysis, we validated the primary regulatory interactions governing this process. We identified a novel regulatory scheme wherein environmentally responsive genes, and , activate , modulating the nitrogen metabolism regulators fnr and nac. This regulatory cascade controls the stress regulators and , ultimately affecting the cell motility gene , unveiling a novel regulatory axis that elucidates the complex regulatory dynamics during the AAT process. Our approach, merging empirical data with prior knowledge, represents a significant advance in modeling cellular signaling processes, offering a deeper understanding of microbial physiology and its applications in biotechnology.
Topics: Escherichia coli; Algorithms; Gene Expression Regulation, Bacterial; Anaerobiosis; Aerobiosis; Gene Regulatory Networks; Escherichia coli Proteins; Signal Transduction; Models, Biological; Gene Expression Profiling
PubMed: 38891842
DOI: 10.3390/ijms25115654 -
Ecotoxicology and Environmental Safety Jul 2024Simultaneous heterotrophic nitrification and aerobic denitrification (SND) is gaining tremendous attention due to its high efficiency and low cost in water treatment....
Simultaneous heterotrophic nitrification and aerobic denitrification (SND) is gaining tremendous attention due to its high efficiency and low cost in water treatment. However, SND on an industrial scale is still immature since effects of coexisting pollutants, for example, heavy metals, on nitrogen removal remains largely unresolved. In this study, a HNAD bacterium (Pseudomonas sp. XF-4) was isolated. It could almost completely remove ammonium and nitrate at pH 5-9 and temperature 20 ℃-35 ℃ within 10 h, and also showed excellently simultaneous nitrification and denitrification efficiency under the coexistence of any two of inorganic nitrogen sources with no intermediate accumulation. XF-4 could rapidly grow again after ammonium vanish when nitrite or nitrate existed. There was no significant effects on nitrification and denitrification when Cd(II) was lower than 10 mg/L, and 95 % of Cd(II) was removed by XF-4. However, electron carrier and electron transport system activity was inhibited, especially at high concentration of Cd(II). Overall, this study reported a novel strain capable of simultaneous nitrification and denitrification coupled with Cd(II) removal efficiently. The results provided new insights into treatment of groundwater or wastewater contaminated by heavy metals and nitrogen.
Topics: Cadmium; Denitrification; Nitrification; Pseudomonas; Water Pollutants, Chemical; Nitrogen; Heterotrophic Processes; Nitrates; Wastewater; Biodegradation, Environmental; Aerobiosis; Water Purification; Ammonium Compounds
PubMed: 38878332
DOI: 10.1016/j.ecoenv.2024.116588 -
Water Science and Technology : a... Jun 2024To assess the possibility of using aerobic denitrification (AD) bacteria with high NO-N accumulation for nitrogen removal in wastewater treatment, conditional...
To assess the possibility of using aerobic denitrification (AD) bacteria with high NO-N accumulation for nitrogen removal in wastewater treatment, conditional optimization, as well as sole and mixed nitrogen source tests involving AD bacterium, sp. pw-6 was performed. The results showed that the optimal carbon source, pH, / ratio, rotational speed, and salinity for this strain were determined to be succinate, 7, 20, 160 rpm, and 0%, respectively. Further, this strain preferentially utilized NH-N, NO-N, and NO-N, and when NO-N was its sole nitrogen source, 92.28% of the NO-N (150 mg·L) was converted to NO-N. However, when NH-N and NO-N constituted the mixed nitrogen source, NO-N utilization by this strain was significantly lower ( < 0.05). Therefore, a strategy was proposed to combine pw-6 bacteria with traditional autotrophic nitrification to achieve the application of pw-6 bacteria in NH-N-containing wastewater treatment. Bioaugmented application experiments showed significantly higher NH-N removal (5.96 ± 0.94 mg·L·h) and lower NO-N accumulation (2.52 ± 0.18 mg·L·h) rates ( < 0.05) than those observed for the control test. Thus, AD bacteria with high NO-N accumulation can also be used for practical applications, providing a basis for expanding the selection range of AD strains for wastewater treatment.
Topics: Nitrogen; Comamonas; Denitrification; Waste Disposal, Fluid; Wastewater; Aerobiosis; Water Purification; Water Pollutants, Chemical
PubMed: 38877627
DOI: 10.2166/wst.2024.176 -
Water Science and Technology : a... Jun 2024In this study, three sequencing batch biofilter granular reactors (SBBGRs) were employed to treat model lignin wastewater containing different lignin models...
In this study, three sequencing batch biofilter granular reactors (SBBGRs) were employed to treat model lignin wastewater containing different lignin models (2,6-dimethoxyphenol, 4-methoxyphenol, and vanillin). After 40 days of cultivation, uniform-shaped aerobic granular sludge (AGS) was successfully developed through nutrient supplementation with synthetic wastewater. During the acclimation stage, the chemical oxygen demand (COD) reduction efficiencies of the three reactors showed a trend of initial decreasing (5-20%) and then recovering to a high reduction efficiency (exceeding 90%) in a short period of time. During the stable operation stage, all three reactors achieved COD reduction efficiencies exceeding 90%. These findings indicated the cultivated AGS's robust resistance to changes in lignin models in water. UV-Vis spectra analysis confirmed the effective degradation of the three lignin models. Microbiological analysis showed that and were always the dominant phyla. At the genus level, while (15.46%) dominated in the inoculation sludge, (7.93%), (11.77%), and (25.37%) were dominant in the three reactors (for 2,6-dimethoxyphenol, 4-methoxyphenol, and vanillin) after degradation, respectively. These findings demonstrate that AGS cultured with SBBGR effectively degrades lignin models, with different dominant strains observed for various lignin models.
Topics: Sewage; Lignin; Bioreactors; Aerobiosis; Filtration; Waste Disposal, Fluid; Bacteria
PubMed: 38877621
DOI: 10.2166/wst.2024.161 -
The ISME Journal Jan 2024Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing... (Review)
Review
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
Topics: Methane; Oxidation-Reduction; Aerobiosis; Metabolic Networks and Pathways; Models, Biological
PubMed: 38861460
DOI: 10.1093/ismejo/wrae102 -
Journal of Hazardous Materials Aug 2024The effects of antibiotics, such as tetracycline, sulfamethoxazole, and ciprofloxacin, on functional microorganisms are of significant concern in wastewater treatment....
The effects of antibiotics, such as tetracycline, sulfamethoxazole, and ciprofloxacin, on functional microorganisms are of significant concern in wastewater treatment. This study observed that Acinetobacter indicus CZH-5 has a limited capacity to remove nitrogen and phosphorus using antibiotics (5 mg/L) as the sole carbon source. When sodium acetate was supplied (carbon/nitrogen ratio = 7), the average removal efficiencies of ammonia-N, total nitrogen, and orthophosphate-P increased to 52.46 %, 51.95 %, and 92.43 %, respectively. The average removal efficiencies of antibiotics were 84.85 % for tetracycline, 39.32 % for sulfamethoxazole, 18.85 % for ciprofloxacin, and 23.24 % for their mixtures. Increasing the carbon/nitrogen ratio to 20 further improved the average removal efficiencies to 72.61 % for total nitrogen and 97.62 % for orthophosphate-P (5 mg/L antibiotics). Additionally, the growth rate and pollutant removal by CZH-5 were unaffected by the presence of 0.1-1 mg/L antibiotics. Transcriptomic analysis revealed that the promoted translation of aceE, aarA, and gltA genes provided ATP and proton -motive forces. The nitrogen metabolism and polyphosphate genes were also affected. The expression of acetate kinase, dehydrogenase, flavin mononucleotide enzymes, and cytochrome P450 contributed to antibiotic degradation. Intermediate metabolites were investigated to determine the reaction pathways.
Topics: Nitrogen; Phosphorus; Anti-Bacterial Agents; Acinetobacter; Water Pollutants, Chemical; Aerobiosis; Biodegradation, Environmental; Waste Disposal, Fluid; Wastewater
PubMed: 38850942
DOI: 10.1016/j.jhazmat.2024.134831 -
Chemosphere Aug 2024Octylphenol polyethoxylates (OPEO) are composed of a hydrophobic octylphenol (OP) group and a hydrophilic polyethylene oxide (EO) chain and are widely used in commercial...
Octylphenol polyethoxylates (OPEO) are composed of a hydrophobic octylphenol (OP) group and a hydrophilic polyethylene oxide (EO) chain and are widely used in commercial products. Shorter EO chains and OPEO biometabolites have been identified as endocrine-disrupting contaminants and can threaten biotic factors in the ecosystem. In this study, OPEO at three EO lengths (TX-45, TX-114, and TX-165) were selected in monomer (MN) or micelle (MC) state for batch experiments under aerobic conditions, with results showing biodegradation rates of 90 % within 35-70 h. The pseudo-first-order constant (k) of OPEO biodegradation was observed in the order TX-45 (0.1414 h) > TX-114 (0.0556 h) > TX-165 (0.0485 h), with biomineralisation reaching at least 80 % for all OPEO. The selective biodegradation of EO chains was also measured, with initial accumulation of OPEO observed along with the depletion of longer EO chains for TX-45 and TX-114 in both the MN and MC states. A similar trend was observed for the MN state of TX-165, with OPEO-OPEO observed to accumulate and reduced after 70 h. MC biodegradation was accomplished via the initial accumulation of OPEO-OPEO. The amounts of OPEO increased and others reduced; however, OPEO remained high at the end of biodegradation for TX-165. Bacterial community analysis indicated that the genera Sphingobium spp., Pseudomonas spp., Flavobacterium spp., Comamonas spp., and Sphingopyxis spp. dominate OPEO biodegradation, and they have their roles during biodegradation, and the community-level physiological profile (CLPP) was also changed by biodegradation in both the MN and MC states.
Topics: Biodegradation, Environmental; Phenols; Polyethylene Glycols; Bacteria; Aerobiosis; Endocrine Disruptors
PubMed: 38844102
DOI: 10.1016/j.chemosphere.2024.142538 -
Chemosphere Aug 2024Pseudomonas sp. ZHL02, removing nitrogen via ammonia nitrogen (NH) → hydroxylamine (HNOH) → nitrite (NO) → nitrate (NO) → NO → nitric oxide (NO) → nitrous...
Pseudomonas sp. ZHL02, removing nitrogen via ammonia nitrogen (NH) → hydroxylamine (HNOH) → nitrite (NO) → nitrate (NO) → NO → nitric oxide (NO) → nitrous oxide (NO) pathway was employed for getting in-depth information on the heterotrophic nitrification-aerobic denitrification (HNAD) pathway from carbon oxidation, nitrogen conversion, electron transport process, enzyme activity, as well as gene expression while sodium succinate, sodium citrate, and sodium acetate were utilized as the carbon sources. The nitrogen balance analysis results demonstrated that ZHL02 mainly removed NH-N through assimilation. The carbon source metabolism resulted in the discrepancies in electron transport chain and nitrogen removal between different HNAD bacteria. Moreover, the prokaryotic strand-specific transcriptome method showed that, amo and hao were absent in ZHL02, and unknown genes may be involved in ZHL02 during the HNAD process. As a fascinating process for removing nitrogen, the HNAD process is still puzzling, and the relationship between carbon metabolism and nitrogen metabolism among different HNAD pathways should be studied further.
Topics: Denitrification; Nitrification; Carbon; Nitrogen; Heterotrophic Processes; Pseudomonas; Aerobiosis; Nitrites; Nitrates
PubMed: 38838867
DOI: 10.1016/j.chemosphere.2024.142525 -
Scientific Reports Jun 2024In this work, the effect of moderate electromagnetic fields (2.5, 10, and 15 mT) was studied using an immersed coil inserted directly into a bioreactor on batch...
In this work, the effect of moderate electromagnetic fields (2.5, 10, and 15 mT) was studied using an immersed coil inserted directly into a bioreactor on batch cultivation of yeast under both aerobic and anaerobic conditions. Throughout the cultivation, parameters, including CO levels, O saturation, nitrogen consumption, glucose uptake, ethanol production, and yeast growth (using OD 600 measurements at 1-h intervals), were analysed. The results showed that 10 and 15 mT magnetic fields not only statistically significantly boosted and sped up biomass production (by 38-70%), but also accelerated overall metabolism, accelerating glucose, oxygen, and nitrogen consumption, by 1-2 h. The carbon balance analysis revealed an acceleration in ethanol and glycerol production, albeit with final concentrations by 22-28% lower, with a more pronounced effect in aerobic cultivation. These findings suggest that magnetic fields shift the metabolic balance toward biomass formation rather than ethanol production, showcasing their potential to modulate yeast metabolism. Considering coil heating, opting for the 10 mT magnetic field is preferable due to its lower heat generation. In these terms, we propose that magnetic field can be used as novel tool to increase biomass yield and accelerate yeast metabolism.
Topics: Saccharomyces cerevisiae; Biomass; Aerobiosis; Fermentation; Anaerobiosis; Ethanol; Magnetic Fields; Glucose; Bioreactors; Glycerol; Oxygen; Nitrogen
PubMed: 38834614
DOI: 10.1038/s41598-024-63628-1