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Variation in the condition of marine sediments provides selective preservation milieus, which act as a key determinant for the abundance and distribution of dinoflagellate resting cysts in natural sediments. Microbial degradation is an understudied biological factor of potential importance in the processes. However, gaps remain in our knowledge about the fundamental information of the bacterial consortia associated with dinoflagellate resting cysts both in laboratory cultures and in the field. Here we used Scrippsiella acuminata as a representative of cyst-producing dinoflagellates to delineate the diversity and composition of bacterial microbiomes co-existing with the laboratory-cultured resting cysts, and to explore possible impacts of low temperature, darkness, and anoxia (the mock conditions commonly observed in marine sediments) on the associated bacterial consortia. Bacterial microbiome with high diversity were revealed associated with S. acuminata at resting stage. The mock conditions could significantly shift bacterial community structure and exert notably inhibitory effects on growth-promoting bacteria. Resting cysts under conditions typically observed in marine sediments fostered bacterial microbiomes with more diverse trophic strategies, characteristic of prominently enriched anaerobic chemotrophic bacteria generating energy via respiration with several different terminal electron acceptors, which yielded more acidic milieu unfavorable for the preservation of calcareous resting cysts. Our findings suggest that there is complex and dynamic interaction between dinoflagellates resting cysts and the associated bacterial consortia in natural sediments. This intrinsic interaction may influence the maintenance and/or accumulation of dinoflagellate resting cysts with potential of germination and initiation blooms in the field. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. We found that the planktonic bacteria under OS conditions overexpressed quorum sensing genes that are important for the bacteria to communicate with each other, antioxidant stress genes important to reduce OS in the microenvironment for survival, biofilm formation genes and virulence genes. Additionally, we performed RNAseq in vivo and identified the activation of novel genes/pathways of the Type VI Secretion System (T6SS) involved in RPA pathogenicity. In conclusion, RPA appears to survive the high OS microenvironment in chronic wounds and colonizes these wounds by turning on virulence, biofilm-forming and survival genes. These findings reveal pathways that may be promising targets for new therapies aimed at disrupting PA-containing biofilms immediately after debridement to facilitate the treatment of chronic human wounds. [ABSTRACT FROM AUTHOR]

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Many microorganisms are capable of anaerobic respiration in the absence of oxygen, by using different organic compounds as terminal acceptors in electron transport chain. We identify here an anaerobic respiratory chain protein responsible for acrylate reduction in the marine bacterium Shewanella woodyi. When the periplasmic proteins of S. woodyi were separated by ion exchange chromatography, acrylate reductase activity copurified with an ArdA protein (Swoo_0275). Heterologous expression of S. woodyiardA gene (swoo_0275) in Shewanella oneidensis MR-1 cells did not result in the appearance in them of periplasmic acrylate reductase activity, but such activity was detected when the ardA gene was co-expressed with an ardB gene (swoo_0276). Together, these genes encode flavocytochrome c ArdAB, which is thus responsible for acrylate reduction in S. woodyi cells. ArdAB was highly specific for acrylate as substrate and reduced only methacrylate (at a 22-fold lower rate) among a series of other tested 2-enoates. In line with these findings, acrylate and methacrylate induced ardA gene expression in S. woodyi under anaerobic conditions, which was accompanied by the appearance of periplasmic acrylate reductase activity. ArdAB-linked acrylate reduction supports dimethylsulfoniopropionate-dependent anaerobic respiration in S. woodyi and, possibly, other marine bacteria. [ABSTRACT FROM AUTHOR]

Geobacter sp. strain SVR uses antimonate [Sb(V)] as a terminal electron acceptor for anaerobic respiration. Here, we visualized a possible key enzyme, periplasmic Sb(V) reductase (Anr), via active staining and non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that a novel dimethyl sulfoxide (DMSO) reductase family protein, WP_173201954.1, is involved in Anr. This protein was closely related with AnrA, a protein suggested to be the catalytic subunit of a respiratory Sb(V) reductase in Desulfuribacillus stibiiarsenatis. The anr genes of strain SVR (anrXSRBAD) formed an operon-like structure, and their transcription was upregulated under Sb(V)-respiring conditions. The expression of anrA gene was induced by more than 1 μM of antimonite [Sb(III)]; however, arsenite [As(III)] did not induce the expression of anrA gene. Tandem mass tag-based proteomic analysis revealed that, in addition to Anr proteins, proteins in the following categories were upregulated under Sb(V)-respiring conditions: (i) Sb(III) efflux systems such as Ant and Ars; (ii) antioxidizing proteins such as ferritin, rubredoxin, and thioredoxin; (iii) protein quality control systems such as HspA, HslO, and DnaK; and (iv) DNA repair proteins such as UspA and UvrB. These results suggest that strain SVR copes with antimony stress by modulating pleiotropic processes to resist and actively metabolize antimony. To the best of our knowledge, this is the first report to demonstrate the involvement of AnrA in Sb(V) respiration at the protein level. Furthermore, this is the first example to show high expression of the Ant system proteins in the Sb(V)-respiring bacterium. IMPORTANCE Antimony (Sb) exists mainly as antimonite [Sb(III)] or antimonate [Sb(V)] in the environment, and Sb(III) is more toxic than Sb(V). Recently, microbial involvement in Sb redox reactions has received attention. Although more than 90 Sb(III)-oxidizing bacteria have been reported, information on Sb(V)-reducing bacteria is limited. Especially, the enzyme involved in dissimilatory Sb(V) reduction, or Sb(V) respiration, is unclear, despite this pathway being very important for the circulation of Sb in nature. In this study, we demonstrated that the Sb(V) reductase (Anr) of an Sb(V)-respiring bacterium (Geobacter sp. SVR) is a novel member of the dimethyl sulfoxide (DMSO) reductase family. In addition, we found that strain SVR copes with Sb stress by modulating pleiotropic processes, including the Ant and Ars systems, and upregulating the antioxidant and quality control protein levels. Considering the abundance and diversity of putative anr genes in the environment, Anr may play a significant role in global Sb cycling in both marine and terrestrial environments. [ABSTRACT FROM AUTHOR]

【Objective】Fresh bamboo shoots are bamboo shoot products that have not been blanched or pickled, with a crispy taste and refreshing flavor. However, fresh bamboo shoots breathe vigorously, which are prone to dehydration and wilting, making them difficult to keep fresh, thus affecting their sales. Spontaneous modified atmosphere packaging reduces the respiratory intensity of packaged fruits and vegetables by regulating the gas composition of the internal environment. Studying the effects of different modified atmosphere packaging treatments on the postharvest storage quality and lignification of fresh bamboo shoots could provide references for the selection of fresh-keeping packaging for fresh bamboo shoots.【Method】The peeled fresh bamboo shoots were packed in the spontaneous modified atmosphere preservation bag (thickness 20μm, O2transmission rate 11 643 cm3/m2·d·atm, water vapor transmission rate 62.586 g/m2·d), and the vacuum bag made of nylon was used as control. The packaged fresh bamboo shoots were stored in the cold storage to study the quality change and the difference of lignification degree during storage.【Result】Compared with traditional vacuum preservation techniques, spontaneous modified atmosphere packaging could significantly reduce the respiratory intensity of fresh bamboo shoots during storage by creating a low oxygen and low carbon dioxide(O2 < 5%, CO2 < 5%) environment inside the bag through the respiration of the bamboo shoots themselves and the gas permeability of the membrane material. The peak intensity was only 46.93% of that of vacuum treatment. After 21 days of storage, modified atmosphere packaging significantly inhibited the browning and membrane lipid peroxidation of bamboo shoots. The brightness of the core of packaged bamboo shoots decreased by only 6.17% compared with that upon harvest, while that of vacuum packaging decreased by 17.74%. The content of malondialdehyde in vacuum packaged bamboo shoots was 2.93 times that in modified atmosphere packaging. In terms of lignification, the lignification rates of bamboo shoots in two types of packaging began to increase after 14 days of storage. The activities of key enzymes for lignification of bamboo shoots (phenylalanine ammonia lyase, peroxidase, cinnamon dehydrogenase) peaked in vacuum packaging, and lignification intensified; however, there was no peak in the related enzyme activity of bamboo shoots in the modified atmosphere packaging, and the enzyme activity increased slowly, delaying the lignification of bamboo shoot and maintaining the crisp taste of the bamboo shoots. After 21 days of storage, the lignin content of packaged bamboo shoots decreased by 15.01% compared to vacuum packaged bamboo shoots, effectively extending the freshness period of fresh bamboo shoots.【Conclusion】The low oxygen and low carbon dioxide gas environment in the spontaneous modified atmosphere packaging bag is conducive to the storage of fresh bamboo shoots, and the quality and nutrient content are significantly better than those of vacuum packaging treatment. It has a good market prospect for fresh bamboo shoots.

Genes of putative reductases of α,β-unsaturated carboxylic acids are abundant among anaerobic and facultatively anaerobic microorganisms, yet substrate specificity has been experimentally verified for few encoded proteins. Here, we co-produced in Escherichia coli a heterodimeric protein of the facultatively anaerobic marine bacterium Vibrio ruber (GenBank SJN56019 and SJN56021; annotated as NADPH azoreductase and urocanate reductase, respectively) with Vibrio cholerae flavin transferase. The isolated protein (named Crd) consists of the sjn56021-encoded subunit CrdB (NADH:flavin, FAD binding 2, and FMN bind domains) and an additional subunit CrdA (SJN56019, a single NADH:flavin domain) that interact via their NADH:flavin domains (Alphafold2 prediction). Each domain contains a flavin group (three FMNs and one FAD in total), one of the FMN groups being linked covalently by the flavin transferase. Crd readily reduces cinnamate, p-coumarate, caffeate, and ferulate under anaerobic conditions with NADH or methyl viologen as the electron donor, is moderately active against acrylate and practically inactive against urocanate and fumarate. Cinnamates induced Crd synthesis in V. ruber cells grown aerobically or anaerobically. The Crd-catalyzed reduction started by NADH demonstrated a time lag of several minutes, suggesting a redox regulation of the enzyme activity. The oxidized enzyme is inactive, which apparently prevents production of reactive oxygen species under aerobic conditions. Our findings identify Crd as a regulated NADH-dependent cinnamate reductase, apparently protecting V. ruber from (hydroxy)cinnamate poisoning. [ABSTRACT FROM AUTHOR]

[Objective] Fresh bamboo shoots are bamboo shoot products that have not been blanched or pickled, with a crispy taste and refreshing flavor. However, fresh bamboo shoots breathe vigorously, which are prone to dehydration and wilting, making them difficult to keep fresh, thus affecting their sales. Spontaneous modified atmosphere packaging reduces the respiratory intensity of packaged fruits and vegetables by regulating the gas composition of the internal environment. Studying the effects of different modified atmosphere packaging treatments on the postharvest storage quality and lignification of fresh bamboo shoots could provide references for the selection of fresh-keeping packaging for fresh bamboo shoots. [Method] The peeled fresh bamboo shoots were packed in the spontaneous modified atmosphere preservation bag (thickness 20 μm, O2 transmission rate 11 643 cm³ /m² ·d·atm, water vapor transmission rate 62.586 g/m² ·d), and the vacuum bag made of nylon was used as control. The packaged fresh bamboo shoots were stored in the cold storage to study the quality change and the difference of lignification degree during storage. [Result] Compared with traditional vacuum preservation techniques, spontaneous modified atmosphere packaging could significantly reduce the respiratory intensity of fresh bamboo shoots during storage by creating a low oxygen and low carbon dioxide (O2 <5%, CO2 <5%) environment inside the bag through the respiration of the bamboo shoots themselves and the gas permeability of the membrane material. The peak intensity was only 46.93% of that of vacuum treatment. After 21 days of storage, modified atmosphere packaging significantly inhibited the browning and membrane lipid peroxidation of bamboo shoots. The brightness of the core of packaged bamboo shoots decreased by only 6.17% compared with that upon harvest, while that of vacuum packaging decreased by 17.74%. The content of malondialdehyde in vacuum packaged bamboo shoots was 2.93 times that in modified atmosphere packaging. In terms of lignification, the lignification rates of bamboo shoots in two types of packaging began to increase after 14 days of storage. The activities of key enzymes for lignification of bamboo shoots (phenylalanine ammonia lyase, peroxidase, cinnamon dehydrogenase) peaked in vacuum packaging, and lignification intensified; however, there was no peak in the related enzyme activity of bamboo shoots in the modified atmosphere packaging, and the enzyme activity increased slowly, delaying the lignification of bamboo shoot and maintaining the crisp taste of the bamboo shoots. After 21 days of storage, the lignin content of packaged bamboo shoots decreased by 15.01% compared to vacuum packaged bamboo shoots, effectively extending the freshness period of fresh bamboo shoots. [Conclusion] The low oxygen and low carbon dioxide gas environment in the spontaneous modified atmosphere packaging bag is conducive to the storage of fresh bamboo shoots, and the quality and nutrient content are significantly better than those of vacuum packaging treatment. It has a good market prospect for fresh bamboo shoots. [ABSTRACT FROM AUTHOR]

Denitrification is a form of anaerobic respiration wherein nitrate (NO3 -) is sequentially reduced via nitrite (NO2 -), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2 - to N2, and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N2O reduction required supplementation with a denitri fication intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3 - served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter, we found that NO3 - acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2 - but not NO3 - activated N2O reduction, but NO2 - was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. [ABSTRACT FROM AUTHOR]

This review analyzes current information about the anaerobic type of respiration using a synthetic methacrylate compound as an electron acceptor. Both the methacrylate redox systems themselves and the anaerobic bacteria in whose cells they are found are considered. These complexes consist of flavin-containing reductase and multiheme cytochrome c3 variants. The genes of the components of the methacrylate redox systems of different microorganisms are homologous and are organized into one operon. Methacrylate-reducing activity is determined in the periplasm. The only known bacterial acrylate reductase that reduces the natural compound differs from methacrylate redox systems. The physiological role, origin, and research perspectives for this unique enzyme system are discussed. [ABSTRACT FROM AUTHOR]

Bipolar disorder (BD) is one of the major psychiatric diseases in which the impairment of mitochondrial functions has been closely connected or associated with the disease pathologies. Different lines of evidence of the close connection between mitochondria dysfunction and BD were discussed with a particular focus on (1) dysregulation of energy metabolism, (2) effect of genetic variants, (3) oxidative stress, cell death and apoptosis, (4) dysregulated calcium homeostasis and electrophysiology, and (5) current as well as potential treatments targeting at restoring mitochondrial functions. Currently, pharmacological interventions generally provide limited efficacy in preventing relapses or recovery from mania or depression episodes. Thus, understanding mitochondrial pathology in BD will lead to novel agents targeting mitochondrial dysfunction and formulating new effective therapy for BD.

ABSTRACTThe expression of most molybdoenzymes in Escherichia coli has so far been revealed to be regulated by anaerobiosis and requires the presence of iron, based on the necessity of the transcription factor FNR to bind one [4Fe-4S] cluster. One exception is trimethylamine-N-oxide reductase encoded by the torCAD operon, which has been described to be expressed independently from FNR. In contrast to other alternative anaerobic respiratory systems, the expression of the torCAD operon was shown not to be completely repressed by the presence of dioxygen. To date, the basis for the O2-dependent expression of the torCAD operon has been related to the abundance of the transcriptional regulator IscR, which represses the transcription of torS and torT, and is more abundant under aerobic conditions than under anaerobic conditions. In this study, we reinvestigated the regulation of the torCAD operon and its dependence on the presence of iron and identified a novel regulation that depends on the presence of the bis-molybdopterin guanine dinucleotide (bis-MGD) molybdenum cofactor . We confirmed that the torCAD operon is directly regulated by the heme-containing protein TorC and is indirectly regulated by ArcA and by the availability of iron via active FNR and Fur, both regulatory proteins that influence the synthesis of the molybdenum cofactor. Furthermore, we identified a novel regulation mode of torCAD expression that is dependent on cellular levels of bis-MGD and is not used by other bis-MGD-containing enzymes like nitrate reductase.IMPORTANCEIn bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. FNR is a very important transcription factor that represents the master switch for the expression of target genes in response to anaerobiosis. Only Escherichia coli trimethylamine-N-oxide (TMAO) reductase escapes this regulation by FNR. We identified that the expression of TMAO reductase is regulated by the amount of bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor synthesized by the cell itself, representing a novel regulation pathway for the expression of an operon coding for a molybdoenzyme. Furthermore, TMAO reductase gene expression is indirectly regulated by the presence of iron, which is required for the production of the bis-MGD cofactor in the cell.

Previous studies have deciphered the genomic basis of host‐symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae—a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep‐sea and shallow‐water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free‐living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well‐adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen‐adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves. [ABSTRACT FROM AUTHOR]

Chitin is one of the most abundant polymers in nature, with chitinous biomass often discarded as food waste and marine debris. To explore an effective way to degrade chitin, in this work, anaerobic sludge was inoculated at the anode of a two-chamber microbial fuel cell (MFC), and chitin was degraded via anaerobic respiration and fermentation. The results showed that the anaerobic sludge could degrade chitin under both the anaerobic respiration and fermentation modes, with similar degradation rates (7.10 ± 0.96 and 6.96 ± 0.23 C-mg/L·d−1). The open-circuit voltage and output current density could roughly reflect the degradation of chitin in the MFC. The maximum current density generated through the anaerobic sludge degradation of chitin via anaerobic respiration was 160 mA/m2, and the maximum power density was 26.29 mW/m2. The microbial sequencing results revealed substantially different microbial community profiles, with electroactive bacteria (EAB) flora and fermentative bacteria (Longilinea) as the main microbial groups that degraded chitin via anaerobic respiration and fermentation, respectively. Therefore, anaerobic sludge may be a good choice for the treatment of refractory biomass due to its abundant electroactive and fermentative flora. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. We found that the planktonic bacteria under OS conditions overexpressed quorum sensing genes that are important for the bacteria to communicate with each other, antioxidant stress genes important to reduce OS in the microenvironment for survival, biofilm formation genes and virulence genes. Additionally, we performed RNAseq in vivo and identified the activation of novel genes/pathways of the Type VI Secretion System (T6SS) involved in RPA pathogenicity. In conclusion, RPA appears to survive the high OS microenvironment in chronic wounds and colonizes these wounds by turning on virulence, biofilm-forming and survival genes. These findings reveal pathways that may be promising targets for new therapies aimed at disrupting PA-containing biofilms immediately after debridement to facilitate the treatment of chronic human wounds.

ABSTRACT Campylobacter concisus, an emerging pathogen found throughout the human oral-gastrointestinal tract, is able to grow under microaerobic or anaerobic conditions; in the latter case, N- or S-oxides could be used as terminal electron acceptors (TEAs). Analysis of 23 genome sequences revealed the presence of multiple (at least two and up to five) genes encoding for putative periplasmic N- or S-oxide reductases (N/SORs), all of which are predicted to harbor a molybdopterin (or tungstopterin)-bis guanine dinucleotide (Mo/W-bisPGD) cofactor. Various N- or S-oxides, including nicotinamide N-oxide, trimethylamine N-oxide , biotin sulfoxide, dimethyl sulfoxide, and methionine sulfoxide (MetO), significantly increased anaerobic growth in two C. concisus intestinal strains (13826 and 51562) but not in the C. concisus oral (type) strain 33237. A collection of mutants was generated to determine each N/SOR substrate specificity. Surprisingly, we found that disruption of a single gene, annotated as “bisA” (present in strains Cc13826 and Cc51562 but not in Cc33237), abolished all N-/S-oxide-supported respiration. Furthermore, ΔbisA mutants showed increased sensitivity to oxidative stress and displayed cell envelope abnormalities, suggesting BisA plays a role in protein MetO repair. Indeed, purified recombinant CcBisA was able to successfully repair MetO residues on a commercial protein (β-casein), as shown by mass spectrometry. Our results suggest that BisA plays a dual role in C. concisus, by allowing the pathogen to use N-/S-oxides as TEAs and by repairing periplasmic protein-bound MetO residues, therefore essentially being a periplasmic methionine sulfoxide reductase (Msr). This is the first report of a Mo/W-bisPGD-containing Msr enzyme in a pathogen. IMPORTANCE Campylobacter concisus is an excellent model organism to study respiration diversity, including anaerobic respiration of physiologically relevant N-/S-oxides compounds, such as biotin sulfoxide, dimethyl sulfoxide, methionine sulfoxide (MetO), nicotinamide N-oxide, and trimethylamine N-oxide. All C. concisus strains harbor at least two, often three, and up to five genes encoding for putative periplasmic Mo/W-bisPGD-containing N-/S-oxide reductases. The respective role (substrate specificity) of each enzyme was studied using a mutagenesis approach. One of the N/SOR enzymes, annotated as "BisA", was found to be essential for anaerobic respiration of both N- and S-oxides. Additional phenotypes associated with disruption of the bisA gene included increased sensitivity toward oxidative stress and elongated cell morphology. Furthermore, a biochemical approach confirmed that BisA can repair protein-bound MetO residues. Hence, we propose that BisA plays a role as a periplasmic methionine sulfoxide reductase. This is the first report of a Mo/W-bisPGD-enzyme supporting both N- or S-oxide respiration and protein-bound MetO repair in a pathogen.

Acetogens grow autotrophically and use hydrogen (H 2) as the energy source to fix carbon dioxide (CO 2). This feature can be applied to gas fermentation, contributing to a circular economy. A challenge is the gain of cellular energy from H 2 oxidation, which is substantially low, especially when acetate formation coupled with ATP production is diverted to other chemicals in engineered strains. Indeed, an engineered strain of the thermophilic acetogen Moorella thermoacetica that produces acetone lost autotrophic growth on H 2 and CO 2. We aimed to recover autotrophic growth and enhance acetone production, in which ATP production was assumed to be a limiting factor, by supplementing with electron acceptors. Among the four selected electron acceptors, thiosulfate and dimethyl sulfoxide (DMSO) enhanced both bacterial growth and acetone titers. DMSO was the most effective and was further analyzed. We showed that DMSO supplementation enhanced intracellular ATP levels, leading to increased acetone production. Although DMSO is an organic compound, it functions as an electron acceptor, not a carbon source. Thus, supplying electron acceptors is a potential strategy to complement the low ATP production caused by metabolic engineering and to improve chemical production from H 2 and CO 2. [ABSTRACT FROM AUTHOR]

The number of soil microorganisms affect the fertility of the soil and the processes occurring in the soil microflora. An urgent research problem is the rationale for the use of intensive technologies for the cultivation of sweet corn using progressive methods for obtaining a highly productive crop based on the principles of resource conservation, biologization and ecologization. The purpose of the research is to study the toxicity and biological activity of the soil after sowing sweet corn. The tasks are to determine the biological activity and toxicity of the soil, and comparative impact of agricultural practices in the study of soil toxicity. Two-factor experiment in quadruple repetition. The experiments were carried out on the farm enterprise of Popov S.A., the Chernoyarsky district of the Astrakhan region. The research period was 2009…2015. Determination of biological activity and toxicity was carried out at the beginning of the research in 2009 and 2015. According to the assessment of the intensity of the destruction of cellulose on O.E. Pryazhnikova’s scale biological activity was characterized as strong. A close correlation dependence on experience factors was noted, the relationship between the signs was high and direct. When determining the toxicity of the soil, we came to the conclusion that at the beginning of the research favorable conditions for the development of the studied crop were formed on soils cultivated by moldboard cultivation. According to zero tillage, an increase in soil toxicity was observed, which was expressed in a decrease in seed germination, the mass of seedlings. Revisited in 2015. Soil toxicity after zero tillage decreased in all variants, seed germination increased, on average, by 5...8%. As a result of the accumulation of plant residues on the soil surface, an upper humus layer was formed, leading to a constant penetration of ai r into the soil.

Simple Summary: Considerable interest in the physiology of proliferation has been generated by human cancers. Cancers often share features with other proliferative cells that are exemplified by the Warburg effect, which involves an altered metabolism with less oxygen uptake and greater lactate secretion. While some of the Warburg effect can be rationalized as production of biosynthetic precursors to fuel proliferation, lactate secretion does not fit this paradigm as it wastes these valuable precursors. In this context, examining proliferation in organisms that are capable of anaerobic pathways other than lactate production can be illuminating. Many animal species, and indeed eukaryotes in general, can carry out other bioenergetic reactions that do not use oxygen. These reactions frequently involve mitochondria and employ such seemingly baroque processes as running the Krebs cycle, the metabolic heart of the cell, backwards. Detailed study of these processes may require development of new animal model systems. For example, colonial marine hydroids frequently exhibit a stage in the life cycle that only undergoes cellular proliferation and never produces gametes. In contrast, traditional animal models such as worms, flies, and mice undergo only limited proliferation before gamete production. The crucial unresolved issues related to the Warburg effect could thus be understood. Interest in the physiology of proliferation has been generated by human proliferative diseases, i.e., cancers. A vast literature exists on the Warburg effect, which is characterized by aerobic glycolysis, diminished oxygen uptake, and lactate secretion. While these features could be rationalized via the production of biosynthetic precursors, lactate secretion does not fit this paradigm, as it wastes precursors. Forming lactate from pyruvate allows for reoxidizing cytosolic NADH, which is crucial for continued glycolysis and may allow for maintaining large pools of metabolic intermediates. Alternatively, lactate production may not be adaptive, but rather reflect metabolic constraints. A broader sampling of the physiology of proliferation, particularly in organisms that could reoxidize NADH using other pathways, may be necessary to understand the Warburg effect. The best-studied metazoans (e.g., worms, flies, and mice) may not be suitable, as they undergo limited proliferation before initiating meiosis. In contrast, some metazoans (e.g., colonial marine hydrozoans) exhibit a stage in the life cycle (the polyp stage) that only undergoes mitotic proliferation and never carries out meiosis (the medusa stage performs this). Such organisms are prime candidates for general studies of proliferation in multicellular organisms and could at least complement the short-generation models of modern biology. [ABSTRACT FROM AUTHOR]

Terpenoid quinones are liposoluble redox-active compounds that serve as essential electron carriers and antioxidants. One such quinone, rhodoquinone (RQ), couples the respiratory electron transfer chain to the reduction of fumarate to facilitate anaerobic respiration. This mechanism allows RQ-synthesizing organisms to operate their respiratory chain using fumarate as a final electron acceptor. RQ biosynthesis is restricted to a handful of prokaryotic and eukaryotic organisms, and details of this biosynthetic pathway remain enigmatic. One gene, rquA, was discovered to be required for RQ biosynthesis in Rhodospirillum rubrum. However, the function of the gene product, RquA, has remained unclear. Here, using reverse genetics approaches, we demonstrate that RquA converts ubiquinone to RQ directly. We also demonstrate the first in vivo synthetic production of RQ in Escherichia coli and Saccharomyces cerevisiae, two organisms that do not natively produce RQ. These findings help clarify the complete RQ biosynthetic pathway in species which contain RquA homologs.

ABSTRACT Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.

Although metal redox reactions in soils can strongly affect carbon mineralization and other important soil processes, little is known about temporal variations in this redox cycling. Recently, potentiostatically poised electrodes (fixed-potential electrodes) have shown promise for measuring the rate of oxidation and reduction at a specific reduction potential in situ in riparian soils. Here for the first time, we used these electrodes in unsaturated soils to explore the fine-scale temporal redox fluctuations of both iron and manganese in response to environmental conditions. We used three-electrode systems with working electrodes fixed at 100 mV (vs. SHE) and 400 mV at 50 cm and 70 cm in the valley floor soil of a headwater watershed. Electrodes fixed at 100 mV to mimic iron oxides and at 400 mV to mimic manganese oxides allowed real-time reduction and oxidation rates to be calculated from temporal variations in the electric current. Electrode measurements were compared to soil porewater chemistry, pCO2, pO2, groundwater level, resistivity measurements, and precipitation. The fixed-potential electrodes recorded fluctuations over timescales from minutes to weeks. A consistently negative current was observed at 100 mV (interpreted as oxidation of Fe), while the 400-mV electrode fluctuated between negative and positive currents (Mn oxidation and reduction). When the water table rose above the electrodes, reduction was promoted, but above the water table, rainfall only stimulated oxidation. Precipitation frequency thus drove the multi-day reduction or oxidation events (return interval of 5–10 days). These measurements represent the first direct detections of frequency, period, and amplitude of oxidation and reduction events in unsaturated soils. Fixed-potential electrodes hold promise for accurately exploring the fast-changing biogeochemical impacts of metal redox cycling in soils and represent a significant advance for reactions that have been difficult to quantify. [ABSTRACT FROM AUTHOR]

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Waterlogging (WL) is a major limiting factor in global crop production and seriously limits growth and yield improvement in low-lying rainfed regions. Melatonin (MT) is a vital phytohormone that functions as a "master regulator" in multiple facets related to plant growth and development, in addition to maintaining a potential role in response to stresses. However, the pharmacological role of MT in attenuating waterlogging stress in tomato largely remains elucidated. The objective of the current investigation is to justify the physiological regulatory mechanism of tomato seedlings exposed to WL and the putative functions of MT to mitigate the adverse effects of WL. Tomato seedlings were grown on substrate (peat: vermiculite, 2:1, v/v) and at the 4th leaf stage subjected to waterlogging stress for 10 days and seedlings were foliar sprayed with melatonin during waterlogging stress. The results revealed that WL significantly arrested tomato seedlings growth, and reduced pigment content coincided with enhanced leaf senescence. MT supplementation attenuated WL-induced oxidative damage through increasing osmoprotectants activity, elevating antioxidant enzyme functioning synchronized with inhibiting excess reactive oxygen species (ROS) production. The concentrations of MT (28 %), abscisic acid (ABA, 170 %), and 1-aminocyclopropane-1-carboxylic acid (ACC, 129 %) were increased, while indole acetic acid (IAA, 15 %), jasmonic acid (JA, 55 %) and gibberellic acid (GA 3 , 26 %) content were decreased in only WL seedlings roots relative to control seedlings. The core anaerobic respiration enzyme alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) activity were elevated by 127 % and 163 %, respectively at day 10 in WL+MT received seedlings than control. WL treatment varyingly contributed on nutrient content, as evidenced that N+, K+, and Ca2+ content decreased, whereas Mn2+, Fe2+, and Mg2+ content increased and MT addition reversed their concentrations under similar stress conditions. Exogenous MT promoted WL-tolerance of tomato by positively suppressing respiratory burst oxidase homologs (RBOH)-regulating gene expression while up-regulating ethylene biosynthesis gene transcription. Most importantly, programmed cell death (PCD) regulated enzyme caspase-3 activity concurred with PCD-induced gene (caspase-3 , pirin , TBN1) expression significantly inhibited by MT application. In general, these findings reveal that external supplementation with MT can improve plant tolerance to WL through complex processes and multifaceted mechanisms. [Display omitted] • Melatonin and/or waterlogging triggers anaerobic respiratory enzyme activity. • Melatonin regulates hormonal balance during waterlogging. • Melatonin inhibited PCD activity under waterlogging. • Ethylene biosynthesis gene transcription increased under waterlogging condition. [ABSTRACT FROM AUTHOR]

Chitin is one of the most abundant polymers in nature, with chitinous biomass often discarded as food waste and marine debris. To explore an effective way to degrade chitin, in this work, anaerobic sludge was inoculated at the anode of a two-chamber microbial fuel cell (MFC), and chitin was degraded via anaerobic respiration and fermentation. The results showed that the anaerobic sludge could degrade chitin under both the anaerobic respiration and fermentation modes, with similar degradation rates (7.10 ± 0.96 and 6.96 ± 0.23 C-mg/L·d−1). The open-circuit voltage and output current density could roughly reflect the degradation of chitin in the MFC. The maximum current density generated through the anaerobic sludge degradation of chitin via anaerobic respiration was 160 mA/m2, and the maximum power density was 26.29 mW/m2. The microbial sequencing results revealed substantially different microbial community profiles, with electroactive bacteria (EAB) flora and fermentative bacteria (Longilinea) as the main microbial groups that degraded chitin via anaerobic respiration and fermentation, respectively. Therefore, anaerobic sludge may be a good choice for the treatment of refractory biomass due to its abundant electroactive and fermentative flora.

Considerable effort has been put forth to understand mechanisms by which the microbiota modulates and responds to inflammation. Here, we explored whether oxidation metabolites produced by the host during inflammation, sodium nitrate and trimethylamine oxide, impact the composition of a human stool bacterial population in a gut simulator. We then assessed whether an immune-competent in vitro intestinal model responded differently to spent medium from bacteria exposed to these cues compared to spent medium from a control bacterial population. The host-derived oxidation products were found to decrease levels of Bacteroidaceae and overall microbiota metabolic potential, while increasing levels of proinflammatory Enterobacteriaceae and lipopolysaccharide in bacterial cultures, reflecting shifts that occur in vivo in inflammation. Spent microbiota media induced elevated intracellular mucin levels and reduced intestinal monolayer integrity as reflected in transepithelial electrical resistance relative to fresh medium controls. However, multiplexed cytokine analysis revealed markedly different cytokine signatures from intestinal cultures exposed to spent medium with added oxidation products relative to spent control medium, while cytokine signatures of cultures exposed to fresh media were similar regardless of addition of host-derived cues. Further, the presence of immune cells in the intestinal model was required for this differentiation of cytokine signatures. This study indicates that simple in vitro immune-competent intestinal models can capture bacterial-mammalian cross-talk in response to host-derived oxidation products and supports utility of these systems for mechanistic studies of interactions between the gut microbiome and host in inflammation.

As a facultative anaerobe, Escherichia coli can activate various respiratory chains during anaerobic growth, among which the mode of anaerobic respiration with nitrate allows good energy conservation. NarL is one of the regulatory proteins in the Nar two-component system that regulates anaerobic respiration in E. coli. Previous studies have shown that NarL activates downstream gene regulation through phosphorylation. However, there are few studies on other protein translational modifications that influence the regulatory function of NarL. Herein, we demonstrate that acetylation modification exists on K188 and K192, the two lysine residues involved in contacting to DNA, and the degree of acetylation has significant effects on DNA-binding abilities, thus affecting the anaerobic growth of E. coli. In addition, NarL is mainly regulated by acetyl phosphate, but not by peptidyl-lysine N-acetyltransferase. These results indicate that non-enzymatic acetylation of NarL by AcP is one of the important mechanisms for the nitrate anaerobic respiratory pathway in response to environmental changes, which extends the idea of the mechanism underlying the response of intestinal flora to changes in the intestinal environment. Key points: • Acetylation was found in NarL, which was mainly mediated by AcP. • Non-enzymatic acetylation at K188 and K192 affects NarL binding ability. • Acetylation of NarL K188 and K192 regulates anaerobic nitrate growth of E. coli. [ABSTRACT FROM AUTHOR]

A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2−) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists. [ABSTRACT FROM AUTHOR]

With global climate change, waterlogging stress is becoming more frequent. Waterlogging stress inhibits root growth and physiological metabolism, which ultimately leads to yield loss in wheat. Waterlogging priming has been proven to effectively enhance waterlogging tolerance in wheat. However, it is not known whether waterlogging priming can improve the offspring's waterlogging resistance. Here, wheat seeds that applied waterlogging priming for one generation, two generations and three generations are separately used to test the hypoxia stress tolerance in wheat, and the physiological mechanisms are evaluated. Results found that progeny of primed plants showed higher plant biomass by enhancing the net photosynthetic rate and antioxidant enzyme activity. Consequently, more sugars are transported to roots, providing a metabolic substrate for anaerobic respiration and producing more ATP to maintain the root growth in the progeny of primed plants compared with non-primed plants. Furthermore, primed plants' offspring promote ethylene biosynthesis and further induce the formation of a higher rate of aerenchyma in roots. This study provides a theoretical basis for improving the waterlogging tolerance of wheat. [ABSTRACT FROM AUTHOR]

Anaerobic respiration metabolism plays an essential role in the controlled atmosphere storage process of fruits and vegetables. In this study, the effects different volume fractions of CO2 (5%, 8%, 11%, and 14%) treatments on the indicators' changes including pyruvate, pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH) contents, respiration rates, ethylene release rates of garlic under 4 °C storage were investigated with the fixed O2 volume fraction of 3.5%, in order to study the effects of composite modified atmosphere packaging on anaerobic respiratory metabolic pathways and related physiology of garlic. Results indicated that during storage, the pyruvate contents of garlic decreased continuously, while the PDC and ADH activities showed an increasing trend, and the CO2 volume fractions presented significant effects on enzymes activities, especially when CO2 volume fraction exceeded 8%. The trend of ethylene release rates was similar to that of respiration rates. The peaks appeared first at low volume fractions CO2 storage, and the ethylene release and respiration intensity were continuously increased at high CO2 volume fractions. The comprehensive analysis showed that when garlic bulbs were stored at low temperature (4 °C) and 3.5% O2, the ideal ratio was that the volume fraction of CO2 was not higher than 8%. Under these conditions, the pyruvate metabolism related enzymes activities were effectively inhibited, and the accumulation of harmful substances was reduced, meanwhile the ethylene release rate and respiratory intensity were also inhibited. [ABSTRACT FROM AUTHOR]

Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria. [ABSTRACT FROM AUTHOR]

Interest in the physiology of proliferation has been generated by human proliferative diseases, i.e., cancers. A vast literature exists on the Warburg effect, which is characterized by aerobic glycolysis, diminished oxygen uptake, and lactate secretion. While these features could be rationalized via the production of biosynthetic precursors, lactate secretion does not fit this paradigm, as it wastes precursors. Forming lactate from pyruvate allows for reoxidizing cytosolic NADH, which is crucial for continued glycolysis and may allow for maintaining large pools of metabolic intermediates. Alternatively, lactate production may not be adaptive, but rather reflect metabolic constraints. A broader sampling of the physiology of proliferation, particularly in organisms that could reoxidize NADH using other pathways, may be necessary to understand the Warburg effect. The best-studied metazoans (e.g., worms, flies, and mice) may not be suitable, as they undergo limited proliferation before initiating meiosis. In contrast, some metazoans (e.g., colonial marine hydrozoans) exhibit a stage in the life cycle (the polyp stage) that only undergoes mitotic proliferation and never carries out meiosis (the medusa stage performs this). Such organisms are prime candidates for general studies of proliferation in multicellular organisms and could at least complement the short-generation models of modern biology.

Microbial iodate (IO3–) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO3– to iodide (I–) and microbial methylation of I– to volatile gases. The metal reduction pathway is required for anaerobic IO3– respiration by the gammaproteobacterium Shewanella oneidensis. However, the terminal IO3– reductase and additional enzymes involved in the S. oneidensis IO3– electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; Δ mtrA , Δ mtrA -Δ mtrDEF , Δ mtrA -Δ dmsEF , Δ mtr A-ΔSO4360) and DMSO reductase (Δ dmsB) of S. oneidensis were constructed and examined for anaerobic IO3– reduction activity with either 20 mM lactate or formate as an electron donor. IO3– reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO3– as anaerobic electron acceptor. Only the Δ mtrA mutant displayed a severe deficiency in IO3– reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO3– reduction. The Δ mtrA -Δ dmsEF triple mutant displayed a severe deficiency in IO3– reduction activity with formate as the electron donor, whereas Δ mtrA -Δ mtrDEF and Δ mtr A-ΔSO4360 retained moderate IO3– reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO3– reduction. Furthermore, gene deletion mutant Δ dmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO3– with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO3– terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO3– as an alternate terminal electron acceptor. [ABSTRACT FROM AUTHOR]

Litchi is a highly perishable fruit. Ripe litchi fruit loses quality quickly as they hang on tree, giving a very short hanging life and thus harvest period. This study attempted to explore the roles of cytokinin in regulating fruit ripening and senescence of litchi and examine the possibility of applying cytokinin in "on-tree storage" of the fruit. Exogenous cytokinin, forchlorfenuron (CPPU), was applied at 20 mg L−1 7 weeks after full bloom on litchi (Litchi chinensis cv. Feizixiao) fruit clusters. Color parameters, chlorophylls, anthocyanins, fruit and fruit part weights, total soluble solutes (TSSs), soluble sugars, organic acids, non-anthocyanin flavonoids, ethanol, and also CPPU residue in fruit were traced. CPPU residue was higher but decreased faster in the pericarp than in the aril, where it maintained < 10 μg kg−1. CPPU had no significant effect on fruit weight but tended to increase pericarp weight. The treatment suppressed chlorophyll loss and anthocyanin accumulation in the pericarp, increased non-anthocyanin flavonoids in the aril, but had no significant effects on non-anthocyanin flavonoids in the pericarp and total sugar and organic acids in the aril. As the commercially ripe fruit hanged on tree, TSSs, total sugar, and sucrose decreased with ethanol and acetic acid accumulation in the aril. CPPU significantly suppressed the loss of sucrose and total sugar and the accumulation of ethanol and acetic acid in the aril and inhibited malondialdehyde accumulation in the pericarp of the overripe fruit. Soluble invertase, alcohol dehydrogenase, and pyruvate decarboxylase (PDC) activity and gene expression in the aril were downregulated by CPPU. The results suggest that cytokinin partially suppresses the ripening process in litchi and is effective to slow quality loss in the overripe fruit on tree. [ABSTRACT FROM AUTHOR]

Abstract Background Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions. Results Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa. Conclusions The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.

Microbial iodate (IO3–) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO3– to iodide (I–) and microbial methylation of I– to volatile gases. The metal reduction pathway is required for anaerobic IO3– respiration by the gammaproteobacterium Shewanella oneidensis. However, the terminal IO3– reductase and additional enzymes involved in the S. oneidensis IO3– electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; ΔmtrA, ΔmtrA-ΔmtrDEF, ΔmtrA-ΔdmsEF, ΔmtrA-ΔSO4360) and DMSO reductase (ΔdmsB) of S. oneidensis were constructed and examined for anaerobic IO3– reduction activity with either 20 mM lactate or formate as an electron donor. IO3– reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO3– as anaerobic electron acceptor. Only the ΔmtrA mutant displayed a severe deficiency in IO3– reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO3– reduction. The ΔmtrA-ΔdmsEF triple mutant displayed a severe deficiency in IO3– reduction activity with formate as the electron donor, whereas ΔmtrA-ΔmtrDEF and ΔmtrA-ΔSO4360 retained moderate IO3– reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO3– reduction. Furthermore, gene deletion mutant ΔdmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO3– with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO3– terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO3– as an alternate terminal electron acceptor.

Litchi is a highly perishable fruit. Ripe litchi fruit loses quality quickly as they hang on tree, giving a very short hanging life and thus harvest period. This study attempted to explore the roles of cytokinin in regulating fruit ripening and senescence of litchi and examine the possibility of applying cytokinin in “on-tree storage” of the fruit. Exogenous cytokinin, forchlorfenuron (CPPU), was applied at 20 mg L−1 7 weeks after full bloom on litchi (Litchi chinensis cv. Feizixiao) fruit clusters. Color parameters, chlorophylls, anthocyanins, fruit and fruit part weights, total soluble solutes (TSSs), soluble sugars, organic acids, non-anthocyanin flavonoids, ethanol, and also CPPU residue in fruit were traced. CPPU residue was higher but decreased faster in the pericarp than in the aril, where it maintained < 10 μg kg−1. CPPU had no significant effect on fruit weight but tended to increase pericarp weight. The treatment suppressed chlorophyll loss and anthocyanin accumulation in the pericarp, increased non-anthocyanin flavonoids in the aril, but had no significant effects on non-anthocyanin flavonoids in the pericarp and total sugar and organic acids in the aril. As the commercially ripe fruit hanged on tree, TSSs, total sugar, and sucrose decreased with ethanol and acetic acid accumulation in the aril. CPPU significantly suppressed the loss of sucrose and total sugar and the accumulation of ethanol and acetic acid in the aril and inhibited malondialdehyde accumulation in the pericarp of the overripe fruit. Soluble invertase, alcohol dehydrogenase, and pyruvate decarboxylase (PDC) activity and gene expression in the aril were downregulated by CPPU. The results suggest that cytokinin partially suppresses the ripening process in litchi and is effective to slow quality loss in the overripe fruit on tree.

Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC , and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC. [ABSTRACT FROM AUTHOR]

Anaerobic microbial respiration in suboxic and anoxic environments often involves particulate ferric iron (oxyhydr-)oxides as terminal electron acceptors. To ensure efficient respiration, a widespread strategy among iron-reducing microorganisms is the use of extracellular electron shuttles (EES) that transfer two electrons from the microbial cell to the iron oxide surface. Yet, a fundamental understanding of how EES-oxide redox thermodynamics affect rates of iron oxide reduction remains elusive. Attempts to rationalize these rates for different EES, solution pH, and iron oxides on the basis of the underlying reaction free energy of the two-electron transfer were unsuccessful. Here, we demonstrate that broadly varying reduction rates determined in this work for different iron oxides and EES at varying solution chemistry as well as previously published data can be reconciled when these rates are instead related to the free energy of the less exergonic (or even endergonic) first of the two electron transfers from the fully, two-electron reduced EES to ferric iron oxide. We show how free energy relationships aid in identifying controls on microbial iron oxide reduction by EES, thereby advancing a more fundamental understanding of anaerobic respiration using iron oxides. [ABSTRACT FROM AUTHOR]

Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5 mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84 h in URC. In 92 h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form. [ABSTRACT FROM AUTHOR]

In the process of anaerobic respiration, sulfate reducing bacteria, besides sulfates, can use other electron acceptors: nitrates, nitrites, oxidized forms of heavy metals, in particular, hexavalent chromium, which are harmful for organisms. Selection of pollutant-resistant stains of this kind of bacteria isolated from technogenically altered ecotopes, capable of reductive transformation of various nature pollutants, is an especially relevant task for the creation of new effective remediation biotechnologies. The purpose of this work was to investigate the regularities of usage of sulfate, nitrate or nitrite ions by bacteria of the Desulfovibrio genus, isolated from Yavorivske Lake, at conditions of simultaneous presence in the medium of another electron acceptor – Cr(VI), to establish a succession of electron acceptors’ reduction by investigated sulfidogenic bacteria and to evaluate the efficiency of their possible application in technologies of complex purification of the environment from metal, sulfur and nitrogen compounds. Bacteria were grown under anaerobic conditions for 10 days in Kravtsov-Sorokin medium without Mohr’s salt. To study the efficiency of sulfate, nitrate, or nitrite ions’ reduction at simultaneous presence in the medium of Cr(VI), bacteria were sown in media with Na2SO4×10H2O, NaNO3, NaNO2 or K2Cr2O7 to final SO42–, NO3 –, NO2 – or Cr(VI) concentration in the medium of 3.47 (concentration of SO42– in medium of standard composition) or 1.74, 3.47, 5.21, 6.94, 10.41 mM. Biomass was determined turbidimetrically, and the concentrations of sulfate, nitrate, nitrite, ammonium ions, hydrogen sulfide, Cr(VI), Cr(ІІІ) in cultural liquid were determined by spectrophotometric method. It has been established that Cr(VI) inhibits the biomass accumulation, sulfate ions’ reduction and hydrogen sulfide production by Desulfovibrio sp. after simultaneous introduction into the medium of 3.47 mM SO4 2– and 1.74–10.41 mM Cr(VI). In the medium with the same initial content (3.47 mM) of SO42– and Cr(VI), bacteria reduced 2.1–2.3 times more Cr(VI) than sulfate ions with Cr(III) production at concentrations up to 2.2 times higher than hydrogen sulfide. It has been shown that K2Cr2O7 inhibits the biomass accumulation, the nitrate ions reduction and the ammonium ions production by bacteria after simultaneous addition into the medium of 3.47 mM NO3– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO3– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) of NO3– and Cr(VI) bacteria reduced 1.1–1.3 times more nitrate ions than Cr(VI) with the production of ammonium ions at concentrations up to 1.3 times higher than that of Cr(III). It has been established that K2Cr2O7 inhibits the biomass accumulation, the nitrite ions’ reduction and the ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO2– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO2– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) NO2– and Cr(VI) the reduction of Cr(VI) by bacteria practically did not differ from the reduction of nitrite ions (was only slightly lower – up to 1.1 times), almost the same concentrations of trivalent chromium and ammonium ions in the cultural liquid were detected. The processes of nitrate and nitride reduction, carried out by bacteria of Desulfovibrio genus, were revealed to be less sensitive to the negative influence of sodium dichromate, as compared with the process of sulfate ions’ reduction, which in the medium with 3.47 mM SO42– and 1.74–10.41 mM Cr(VІ) decreased by 3.2–4.6 times as compared with this process in the medium with only Na2SO4×10H2O. The investigated strains of bacteria are adapted to high concentrations of toxic pollutants (up to 10.41 mM) and therefore are promising for application in technologies of complex environment purification from hexavalent chromium, sulfur and nitrogen compounds. [ABSTRACT FROM AUTHOR]

Euglena gracilis produces ATP in the anaerobic mitochondria with concomitant wax ester formation, and NADH is essential for ATP formation and fatty acid synthesis in the mitochondria. This study demonstrated that mitochondrial cofactor conversion by nicotinamide nucleotide transhydrogenase (NNT), converting NADPH/NAD+ to NADP+/NADH, is indispensable for sustaining anaerobic metabolism. Silencing of NNT genes significantly decreased wax ester production and cellular viability during anaerobiosis but had no such marked effects under aerobic conditions. An analogous phenotype was observed in the silencing of the gene encoding a mitochondrial NADP+‐dependent malic enzyme. These results suggest that the reducing equivalents produced in glycolysis are shuttled to the mitochondria as malate, where cytosolic NAD+ regeneration is coupled with mitochondrial NADPH generation. [ABSTRACT FROM AUTHOR]

Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.