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The ISME Journal Dec 2023The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back...
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
Topics: Anaerobiosis; Bacteria; Bacteria, Anaerobic; Archaea; Environment
PubMed: 37872273
DOI: 10.1038/s41396-023-01538-2 -
Chemosphere Nov 2021This is the first study to bring evidence on the anaerobic biodegradation of TBBPA occurring during acidogenesis in domestic sewage at environmentally relevant...
This is the first study to bring evidence on the anaerobic biodegradation of TBBPA occurring during acidogenesis in domestic sewage at environmentally relevant concentrations by complex microbial communities. This was accomplished by continuously operating two anaerobic structured bed reactors (ASTBR) for over 100 days under acidogenic (Acidogenic Reactor, AR) and multistep methanogenic (Methanogenic Reactor, MR) conditions. In the AR, the temporal carbohydrates consumption and the acetic acid production were strongly correlated with TBBPA removal by the Pearson's test. The spatial concentration of TBBPA and carbohydrates along the MR and the kinetic degradation profiles corroborate the AR results. It is hypothesized that TBBPA biodegradation in the studied conditions occurs during acidogenesis via the cometabolism supported by non-specific enzymes and the metabolism (dehalorespiration) established by electrons donors such as H, which are both produced during the macrocomponents breakdown in the early stages of the anaerobic digestion. The TBBPA mass balance showed that approximately 86.8 ± 0.05% and 97 ± 0.01% of the removed TBBPA was biodegraded in the AR and MR, respectively. Furthermore, TBBPA biodegradation went further than reductive debromination as total phenols were detected in the reactors' effluent.
Topics: Anaerobiosis; Biodegradation, Environmental; Polybrominated Biphenyls; Sewage
PubMed: 34116313
DOI: 10.1016/j.chemosphere.2021.130995 -
Archives of Microbiology Dec 2021Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing...
Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
Topics: Acetobacteraceae; Anaerobiosis; Base Composition; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 34528111
DOI: 10.1007/s00203-021-02561-7 -
Methods in Molecular Biology (Clifton,... 2022Genetic manipulation is an essential tool to investigate complex microbiological phenomena. In this chapter we describe the techniques required to transform the model...
Genetic manipulation is an essential tool to investigate complex microbiological phenomena. In this chapter we describe the techniques required to transform the model hyperthermophilic, anaerobic archaeon Thermococcus kodakarensis. T. kodakarensis can support two modes of genetic manipulation, dependent either on homologous recombination into the genome or through retention of autonomously replicating plasmids. The robust genetic system developed in T. kodakarensis offers a variety of selectable and counterselectable markers for complex, accurate and iterative genetic manipulations offering greater flexibility to probe gene function in vivo.
Topics: Anaerobiosis; Plasmids; Thermococcus
PubMed: 36125744
DOI: 10.1007/978-1-0716-2445-6_5 -
Bioengineered Dec 2023A recently strategy applied to anaerobic digestion (AD) is the use of biochar (BC) obtained from the pyrolysis of different organic waste. The PRISMA protocol-based... (Review)
Review
A recently strategy applied to anaerobic digestion (AD) is the use of biochar (BC) obtained from the pyrolysis of different organic waste. The PRISMA protocol-based review of the most recent literature data from 2011-2022 was used in this study. The review focuses on research papers from Scopus® and Web of Knowledge®. The review protocol used permits to identify 169 articles. The review indicated a need for further research in the following challenges on the application of BC in AD: i) to increase the use of BC in developing countries, which produce large and diverse amounts of waste that are the source of production of this additive; ii) to determine the effect of BC on the AD of organic waste under psychrophilic conditions; iii) to apply tools of machine learning or robust models that allow the process optimization; iv) to perform studies that include life cycle and technical-economic analysis that allow identifying the potential of applying BC in AD in large-scale systems; v) to study the effects of BC on the agronomic characteristics of the digestate once it is applied to the soil and vi) finally, it is necessary to deepen in the effect of BC on the dynamics of nitrogen and microbial consortia that affect AD, considering the type of BC used. In the future, it is necessary to search for new solutions in terms of the transport phenomena that occurs in AD with the use of BC using robust and precise mathematical models at full-scale conditions.
Topics: Anaerobiosis; Agriculture; Machine Learning; Microbial Consortia
PubMed: 37712696
DOI: 10.1080/21655979.2023.2252191 -
The Science of the Total Environment Oct 2021The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two...
The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale AO™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH recovery rate and %CH in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.
Topics: Anaerobiosis; Archaea; Bioreactors; Methane; Sewage; Spain
PubMed: 34051504
DOI: 10.1016/j.scitotenv.2021.147869 -
International Journal of Molecular... Dec 2023Plant waste biomass is the most abundant renewable energy resource on Earth. The main problem with utilising this biomass in anaerobic digestion is the long and costly... (Review)
Review
Plant waste biomass is the most abundant renewable energy resource on Earth. The main problem with utilising this biomass in anaerobic digestion is the long and costly stage of degrading its complex structure into simple compounds. One of the promising solutions to this problem is the application of fungi of the genus, which show a high capacity to produce hydrolytic enzymes capable of degrading lignocellulosic biomass before anaerobic digestion. This article discusses the structure of plant waste biomass and the problems resulting from its structure in the digestion process. It presents the methods of pre-treatment of lignocellulose with a particular focus on biological solutions. Based on the latest research findings, key parameters related to the application of sp. as a pre-treatment method are discussed. In addition, the possibility of using the digestate from agricultural biogas plants as a carrier for the multiplication of the sp. fungi, which are widely used in many industries, is discussed.
Topics: Anaerobiosis; Trichoderma; Biofuels; Biomass; Hydrolysis
PubMed: 38139408
DOI: 10.3390/ijms242417576 -
The ISME Journal Oct 2020Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic...
Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20-40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.
Topics: Anaerobiosis; Environmental Monitoring; Foraminifera; Geologic Sediments
PubMed: 32641728
DOI: 10.1038/s41396-020-0708-1 -
Journal of Hazardous Materials Oct 2023The use of phytoremediation as a method for wastewater treatment or removal of pollutants is garnering significant interest and duckweed (DW), a free floating...
The use of phytoremediation as a method for wastewater treatment or removal of pollutants is garnering significant interest and duckweed (DW), a free floating macrophyte, depicts significant potential for the removal of nutrients and toxic compounds from contaminated waters. The present work aimed to develop an integrated process for remediating selenate (Se(VI)) using DW biomass and subsequent use of Se(VI) enriched DW for biogas production. The main objective is to extend the application of selenium (Se) enriched DW biomass for biogas production. Se(VI) enriched DW biomass (Se-DW) gave higher methane production (48.38 ± 3.6 mL gCOD) than control DW biomass (C-DW) (24.46 ± 3.6 mL gCOD). To further enhance methane production, three pre-treatment approaches (acid, alkali and hydrothermal) were assessed and the solid and liquid fractions obtained after pre-treatment were used as a substrate. Pre-treatments increased biogas production in both Se-DW and C-DW than untreated conditions. Liquid fractions gave higher biogas production than solid fractions. In Se-DW, highest biogas production was observed in hydrothermal pre-treated Se-DW, while in C-DW, acid pre-treatment gave higher biogas production. Methane production was shown to be enhanced up to a Se(VI) concentration of 1.7 mg L, whereas a concentration beyond this lowered biogas production.
Topics: Selenic Acid; Selenium; Biofuels; Araceae; Methane; Anaerobiosis
PubMed: 37544177
DOI: 10.1016/j.jhazmat.2023.132134 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Nov 2022Traditionally, amino acids are produced mainly by chemical synthesis or aerobic fermentation. Compared to chemical synthesis, production of amino acids by microbial...
Traditionally, amino acids are produced mainly by chemical synthesis or aerobic fermentation. Compared to chemical synthesis, production of amino acids by microbial fermentation directly uses renewable resources as feedstock and this reduces the dependence on petroleum-based compounds and decreases pollutants generation and toxic substrates usage. Fermentation under aerobic conditions has been used widely for its fast growth and high titers. However, a large amount of carbon is used for cell growth and this results in high biomass but low yield of target chemicals. Unlike the long history of aerobic fermentation, the commercial production of amino acids by anaerobic fermentation is realized only in recent years. It has several advantages such as simpler operation, no need for oxygen supply, and high yield close to the theoretical maximum value. L-alanine is the first amino acid commercially produced by anaerobic fermentation. In this article, we summarize the key technology for anaerobic fermentative production of L-alanine and its commercialization. As it is shown to be low-cost, high-efficiency, and environmental-friendly, anaerobic fermentation is expected to be widely used in industrial process and brings greater economic values and social benefits in the future.
Topics: Anaerobiosis; Fermentation; Alanine; Amino Acids; Technology
PubMed: 37699692
DOI: 10.13345/j.cjb.220594