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Proceedings of the National Academy of... Jun 2024Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic...
Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of strain PF2803, a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen- and sulfur-containing polar head groups, moving beyond a reliance on conventional nonphospholipid types.
Topics: Phosphorus; Sulfur; Lipidomics; Nitrogen; Adaptation, Physiological; Sulfates; Bacteria, Anaerobic; Anaerobiosis
PubMed: 38833476
DOI: 10.1073/pnas.2400711121 -
Gut Microbes 2024The facultative anaerobic Gram-positive bacterium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug...
The facultative anaerobic Gram-positive bacterium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug resistant lineage that causes nosocomial infections. The establishment of high-level intestinal colonization by enterococci represents a critical step of infection. The majority of current research on has been conducted under aerobic conditions, while limited attention has been given to its physiological characteristics in anaerobic environments, which reflects its natural colonization niche in the gut. In this study, a high-density transposon mutant library containing 26,620 distinct insertion sites was constructed. Tn-seq analysis identified six genes that significantly contribute to growth under anaerobic conditions. Under anaerobic conditions, deletion of (encoding Fe-S cluster assembly protein B) results in more extensive and significant impairments on carbohydrate metabolism compared to aerobic conditions. Consistently, the pathways involved in this utilization-restricted carbohydrates were mostly expressed at significantly lower levels in mutant compared to wild-type under anaerobic conditions. Moreover, deletion of or (encoding pyruvate formate lyase-activating protein A) led to failure of gastrointestinal colonization in mice. These findings contribute to our understanding of the mechanisms by which maintains proliferation under anaerobic conditions and establishes colonization in the gut.
Topics: Enterococcus faecium; Animals; Mice; Bacterial Proteins; Anaerobiosis; Iron-Sulfur Proteins; Gastrointestinal Tract; Gastrointestinal Microbiome; Gram-Positive Bacterial Infections; Humans; DNA Transposable Elements; Carbohydrate Metabolism; Female; Acetyltransferases
PubMed: 38831611
DOI: 10.1080/19490976.2024.2359665 -
BMC Biology Jun 2024Hydrogenosomes are a specific type of mitochondria that have adapted for life under anaerobiosis. Limited availability of oxygen has resulted in the loss of the...
BACKGROUND
Hydrogenosomes are a specific type of mitochondria that have adapted for life under anaerobiosis. Limited availability of oxygen has resulted in the loss of the membrane-associated respiratory chain, and consequently in the generation of minimal inner membrane potential (Δψ), and inefficient ATP synthesis via substrate-level phosphorylation. The changes in energy metabolism are directly linked with the organelle biogenesis. In mitochondria, proteins are imported across the outer membrane via the Translocase of the Outer Membrane (TOM complex), while two Translocases of the Inner Membrane, TIM22, and TIM23, facilitate import to the inner membrane and matrix. TIM23-mediated steps are entirely dependent on Δψ and ATP hydrolysis, while TIM22 requires only Δψ. The character of the hydrogenosomal inner membrane translocase and the mechanism of translocation is currently unknown.
RESULTS
We report unprecedented modification of TIM in hydrogenosomes of the human parasite Trichomonas vaginalis (TvTIM). We show that the import of the presequence-containing protein into the hydrogenosomal matrix is mediated by the hybrid TIM22-TIM23 complex that includes three highly divergent core components, TvTim22, TvTim23, and TvTim17-like proteins. The hybrid character of the TvTIM is underlined by the presence of both TvTim22 and TvTim17/23, association with small Tim chaperones (Tim9-10), which in mitochondria are known to facilitate the transfer of substrates to the TIM22 complex, and the coupling with TIM23-specific ATP-dependent presequence translocase-associated motor (PAM). Interactome reconstruction based on co-immunoprecipitation (coIP) and mass spectrometry revealed that hybrid TvTIM is formed with the compositional variations of paralogs. Single-particle electron microscopy for the 132-kDa purified TvTIM revealed the presence of a single ring of small Tims complex, while mitochondrial TIM22 complex bears twin small Tims hexamer. TvTIM is currently the only TIM visualized outside of Opisthokonta, which raised the question of which form is prevailing across eukaryotes. The tight association of the hybrid TvTIM with ADP/ATP carriers (AAC) suggests that AAC may directly supply ATP for the protein import since ATP synthesis is limited in hydrogenosomes.
CONCLUSIONS
The hybrid TvTIM in hydrogenosomes represents an original structural solution that evolved for protein import when Δψ is negligible and remarkable example of evolutionary adaptation to an anaerobic lifestyle.
Topics: Trichomonas vaginalis; Protein Transport; Protozoan Proteins; Mitochondrial Precursor Protein Import Complex Proteins; Mitochondria; Organelles
PubMed: 38825681
DOI: 10.1186/s12915-024-01928-8 -
Chemosphere Aug 2024Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries... (Review)
Review
Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.
Topics: Biodegradation, Environmental; Anaerobiosis; Benzene Derivatives; Benzene; Toluene; Xylenes; Environmental Pollutants; Hydrocarbons, Aromatic
PubMed: 38821131
DOI: 10.1016/j.chemosphere.2024.142490 -
Journal of Environmental Management Jun 2024This works proposes a dynamic thermoeconomic analysis of a liquefied biomethane production plant to meet the fuel demand of a fleet of heavy duty trucks in the south of...
This works proposes a dynamic thermoeconomic analysis of a liquefied biomethane production plant to meet the fuel demand of a fleet of heavy duty trucks in the south of Italy. The biomethane is obtained from the upgrading of the biogas produced by means of anaerobic digestion through a plug flow reactor fed by organic fraction of municipal solid waste. The upgrading of the biogas is realized using a three-stage membrane compression process, producing a 96 % pure biomethane. The biomethane liquefaction is realized using a single-mixed refrigerant process and compared to a Linde cycle process. The whole system is assisted by solar energy to reduce the fossil energy consumption of the process and feed-in tariffs are considered as funding policy. The models for the anaerobic digestion, the biogas upgrading, and the biomethane liquefaction are in detail developed in MatLab. The anaerobic digestion model is based on the ADM1 biological model, integrated with a suitable heat transfer model. The biogas upgrading model is based on a simplified Fick model. The liquefaction model is based on an equivalent two heat-exchangers model, taking into account the transient heat transfer. All the components are then integrated in TRNSYS to perform the dynamic simulation for one operating year of the whole system. Results from the thermoeconomic analysis are outstanding in terms of profitability, showing a payback period of less than 2 years and a Net Present Value of the system of 402 M€. The great environmental impact is also confirmed by a Primary Energy Saving of 91 % and a dramatic reduction of 86 % of the CO equivalent emissions.
Topics: Biofuels; Solar Energy; Methane; Anaerobiosis; Italy; Models, Theoretical
PubMed: 38820789
DOI: 10.1016/j.jenvman.2024.121261 -
The ISME Journal Jan 2024Isolate studies have been a cornerstone for unraveling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered...
Isolate studies have been a cornerstone for unraveling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered ecosystems are generally performed by more than a single microbe and often rely on mutualistic interactions. We demonstrate the rational bottom-up design of synthetic, interdependent co-cultures to achieve concomitant utilization of chlorinated methanes as electron donors and organohalogens as electron acceptors. Specialized anaerobes conserve energy from the catabolic conversion of chloromethane or dichloromethane to formate, H2, and acetate, compounds that the organohalide-respiring bacterium Dehalogenimonas etheniformans strain GP requires to utilize cis-1,2-dichloroethenene and vinyl chloride as electron acceptors. Organism-specific qPCR enumeration matched the growth of individual dechlorinators to the respective functional (i.e. dechlorination) traits. The metabolite cross-feeding in the synthetic (co-)cultures enables concomitant utilization of chlorinated methanes (i.e. chloromethane and dichloromethane) and chlorinated ethenes (i.e. cis-1,2-dichloroethenene and vinyl chloride) without the addition of an external electron donor (i.e. formate and H2). The findings illustrate that naturally occurring chlorinated C1 compounds can sustain anaerobic food webs, an observation with implications for the development of interdependent, mutualistic communities, the sustenance of microbial life in oligotrophic and energy-deprived environments, and the fate of chloromethane/dichloromethane and chlorinated electron acceptors (e.g. chlorinated ethenes) in pristine environments and commingled contaminant plumes.
Topics: Coculture Techniques; Hydrocarbons, Chlorinated; Methane; Chloroflexi; Halogenation; Metabolic Networks and Pathways; Dichloroethylenes; Anaerobiosis
PubMed: 38818735
DOI: 10.1093/ismejo/wrae090 -
Journal of Mathematical Biology May 2024Decline of the dissolved oxygen in the ocean is a growing concern, as it may eventually lead to global anoxia, an elevated mortality of marine fauna and even a mass...
Decline of the dissolved oxygen in the ocean is a growing concern, as it may eventually lead to global anoxia, an elevated mortality of marine fauna and even a mass extinction. Deoxygenation of the ocean often results in the formation of oxygen minimum zones (OMZ): large domains where the abundance of oxygen is much lower than that in the surrounding ocean environment. Factors and processes resulting in the OMZ formation remain controversial. We consider a conceptual model of coupled plankton-oxygen dynamics that, apart from the plankton growth and the oxygen production by phytoplankton, also accounts for the difference in the timescales for phyto- and zooplankton (making it a "slow-fast system") and for the implicit effect of upper trophic levels resulting in density dependent (nonlinear) zooplankton mortality. The model is investigated using a combination of analytical techniques and numerical simulations. The slow-fast system is decomposed into its slow and fast subsystems. The critical manifold of the slow-fast system and its stability is then studied by analyzing the bifurcation structure of the fast subsystem. We obtain the canard cycles of the slow-fast system for a range of parameter values. However, the system does not allow for persistent relaxation oscillations; instead, the blowup of the canard cycle results in plankton extinction and oxygen depletion. For the spatially explicit model, the earlier works in this direction did not take into account the density dependent mortality rate of the zooplankton, and thus could exhibit Turing pattern. However, the inclusion of the density dependent mortality into the system can lead to stationary Turing patterns. The dynamics of the system is then studied near the Turing bifurcation threshold. We further consider the effect of the self-movement of the zooplankton along with the turbulent mixing. We show that an initial non-uniform perturbation can lead to the formation of an OMZ, which then grows in size and spreads over space. For a sufficiently large timescale separation, the spread of the OMZ can result in global anoxia.
Topics: Animals; Oxygen; Zooplankton; Models, Biological; Phytoplankton; Computer Simulation; Oceans and Seas; Plankton; Mathematical Concepts; Ecosystem; Seawater; Food Chain; Anaerobiosis
PubMed: 38801565
DOI: 10.1007/s00285-024-02107-7 -
Bioresource Technology Jul 2024The present work has estimated greenhouse gas emissions in aerobic and anaerobic Wastewater Treatment Plants in Southern Italy. Greenhouse gases emissions from each...
The present work has estimated greenhouse gas emissions in aerobic and anaerobic Wastewater Treatment Plants in Southern Italy. Greenhouse gases emissions from each treatment unit were calculated based on emission factors related to Chemical Oxygen Demand removal for biogenic CO and CH assessment and on Nitrogen removal for NO. NO, biogenic CO and CH emissions vary for aerobic and anaerobic-based WWTPs respectively from 73 kgCO/PE*y for anaerobic plants to 91 kgCO/PE*y for aerobic plants. In aerobic and anaerobic digestion systems WWTPs the contributions to CO total emissions from NO, CH, biogenic CO, and fossil CO are 30 %-33 %, 20 %-29 %, 22 %-25 %, and 26 %-16 %, respectively. NO emissions from biological processes were found the most contributing sources of greenhouse gases while in the physical processes higher contribution is indirect carbon dioxide related to energy consumption. Compensatory measures are reported to reduce greenhouse gases emissions.
Topics: Greenhouse Gases; Wastewater; Carbon Dioxide; Methane; Water Purification; Nitrous Oxide; Anaerobiosis; Greenhouse Effect
PubMed: 38797361
DOI: 10.1016/j.biortech.2024.130897 -
Scientific Reports May 2024Anaerobic co-digestion is an effective method for addressing the issue of a single substrate not being able to achieve optimal conditions for anaerobic digestion. By...
Anaerobic co-digestion is an effective method for addressing the issue of a single substrate not being able to achieve optimal conditions for anaerobic digestion. By adjusting the mixture ratio of sewage sludge and food waste to achieve the optimal carbon to nitrogen ratio, the effectiveness of thermophilic-mesophilic temperature phase anaerobic co-digestion (TPAcD) was evaluated in comparison to single phase mesophilic anaerobic co-digestion (MAcD) and thermophilic anaerobic co-digestion (TAcD). The results indicated that TPAcD increased methane yield by 50.3% and 32.7% compared to MAcD and TAcD, respectively. The variation in VFA, pH, and ammonia nitrogen levels demonstrated that TPAcD combines the advantages of both MAcD and TAcD, with a higher hydrolysis rate in the early stage under thermophilic conditions (55 °C) and a suitable environment in the later stage under mesophilic conditions (35 °C). The kinetic parameters of anaerobic co-digestions also demonstrated that TPAcD performs better. Therefore, further research on TPAcD of sewage sludge and food waste is warranted due to its significant improvements in methane production rate, total methane yield, and system stability. Additionally, TPAcD contributes to reducing carbon emissions and supports the realization of "carbon neutrality".
Topics: Sewage; Anaerobiosis; Methane; Temperature; Bioreactors; Food; Nitrogen; Hydrogen-Ion Concentration; Kinetics; Carbon; Food Loss and Waste
PubMed: 38796540
DOI: 10.1038/s41598-024-62998-w -
Molecules (Basel, Switzerland) May 2024Lignin, the largest non-carbohydrate component of lignocellulosic biomass, is also a recalcitrant component of the plant cell wall. While the aerobic degradation...
Lignin, the largest non-carbohydrate component of lignocellulosic biomass, is also a recalcitrant component of the plant cell wall. While the aerobic degradation mechanism of lignin has been well-documented, the anaerobic degradation mechanism is still largely elusive. In this work, a versatile facultative anaerobic lignin-degrading bacterium, TL3, was isolated from a termite gut, and was found to metabolize a variety of carbon sources and produce a single kind or multiple kinds of acids. The percent degradation of alkali lignin reached 14.8% under anaerobic conditions, and could reach 17.4% in the presence of glucose within 72 h. Based on the results of infrared spectroscopy and 2D nuclear magnetic resonance analysis, it can be inferred that the anaerobic degradation of lignin may undergo the cleavage of the C-O bond (β-O-4), as well as the C-C bond (β-5 and β-β), and involve the oxidation of the side chain, demethylation, and the destruction of the aromatic ring skeleton. Although the anaerobic degradation of lignin by TL3 was slightly weaker than that under aerobic conditions, it could be further enhanced by adding glucose as an electron donor. These results may shed new light on the mechanisms of anaerobic lignin degradation.
Topics: Lignin; Anaerobiosis; Glucose; Klebsiella; Biomass; Biodegradation, Environmental; Animals
PubMed: 38792038
DOI: 10.3390/molecules29102177