Unraveling the arsenite response mechanisms in the facultative anaerobe Aromatoleum sp. CIB.

Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions

Summary This paper examines whether retention of partially hydrolyzed polyacrylamide (HPAM) is different under anaerobic vs. aerobic conditions. Both static (mixing with loose sand) and dynamic methods (corefloods) were used to determine HPAM retention. There are both advantages and disadvantages associated with determining polymer retention with static tests vs. dynamic tests and with aerobic vs. anaerobic conditions. From static-retention measurements, polymer-adsorption values on pure silica sand or Berea sandstone were small, and they showed little difference between experiments conducted aerobically or anaerobically. For both aerobic and anaerobic conditions, HPAM retention increased significantly with increased pyrite or siderite content. Static retention under anaerobic conditions ranged from 45 to 75 µg/g with 1% of either pyrite or siderite to 137–174 µg/g for 10% pyrite or siderite to 1161–1249 µg/g for 100% pyrite or siderite. If iron minerals are present, the most representative polymer-retention results are obtained (for both static and dynamic tests) if conditions are anaerobic. Retention values (from static measurements) under aerobic conditions were commonly twice those determined under anaerobic conditions. If iron minerals are present and retention tests are performed under aerobic conditions, total organic carbon (TOC) or some similar method should be used for polymer detection. Viscosity detection of polymer may provide retention values that are too high (because oxidative degradation can be misinterpreted as polymer retention). For a broad range of siderite content, retention from static tests did not depend on whether dissolved oxygen was present. However, for a broad range of pyrite content, HPAM retention was significantly lower in the absence of dissolved oxygen than under aerobic conditions. These results may be tied to iron solubility. When polymer solutions were mixed with 100% pyrite over the course of 12 hours, 360–480 ppm of iron dissolved into polymer solutions under both aerobic and anaerobic conditions, whereas with 100% siderite, only 0.0–0.6 ppm of iron dissolved. If dynamic methods (i.e., corefloods) are used to determine polymer retention under aerobic conditions, flow rates should be representative of the field application. Rates that are too high lead to underestimation of polymer retention. With 10% pyrite, dynamic retention was 211 µg/g at 6 ft/D vs. 43.2 µg/g at 30 ft/D. In contrast, retention values were fairly consistent (40.6–47.8 µg/g) between 6 and 33 ft/D under anaerobic conditions.

This paper examines whether retention of partially hydrolyzed polyacrylamide (HPAM) is different under anaerobic versus aerobic conditions. Both static (mixing with loose sand) and dynamic methods (core floods) were used to determine HPAM retention. There are both advantages and disadvantages associated with determining polymer retention using static tests versus dynamic tests and using aerobic versus anaerobic conditions. From static retention measurements, polymer adsorption values on pure silica sand or Berea sandstone were small, and they showed little difference between experiments conducted aerobically or anaerobically. For both aerobic and anaerobic conditions, HPAM retention increased significantly with increased pyrite or siderite content. Static retention under anaerobic conditions ranged from 45-75 µg/g with 1% of either pyrite or siderite to 137-174 µg/g for 10% pyrite or siderite to 1161-1249 µg/g for 100% pyrite or siderite. If iron minerals are present, the most representative polymer retention results are obtained (for both static and dynamic tests) if conditions are anaerobic. Retention values (from static measurements) under aerobic conditions were commonly twice those determined under anaerobic conditions. If iron minerals are present and retention tests are performed under aerobic conditions, TOC or some similar method should be used for polymer detection. Viscosity detection of polymer may provide retention values that are too high (because oxidative degradation can be misinterpreted as polymer retention). For a broad range of siderite content, retention from static tests did not depend on whether dissolved oxygen was present. However, for a broad range of pyrite content, HPAM retention was significantly lower in the absence of dissolved oxygen than under aerobic conditions. Theses results may be tied to iron solubility. When polymer solutions were mixed with 100% pyrite over the course of 12 hours, 360–480-ppm iron dissolved into polymer solutions under both aerobic and anaerobic conditions, whereas with 100% siderite, only 0–0.6-ppm iron dissolved. If dynamic methods (i.e., corefloods) are used to determine polymer retention under aerobic conditions, flow rates should be representative of the field application. Rates that are too high lead to underestimation of polymer retention. With 10% pyrite, dynamic retention was 211 μg/g at 6 ft/d versus 43.2 μg/g at 30 ft/d. In contrast, retention values were fairly consistent (40.6 – 47.8 μg/g) between 6 ft/d and 33 ft/d under anaerobic conditions.

The Impact of O2 on the Fe–S Cluster Biogenesis Requirements of Escherichia coli FNR

Fusobacteria have been suspected to be pathobionts of colon cancer and inflammatory bowel disease. However, the immunomodulatory properties that affect these inflammatory reactions in dendritic cells (DCs) under anaerobic and aerobic conditions have not yet been characterized. We directly assessed the stimulatory effects of anaerobic commensal bacteria, including fusobacteria, on a human DC line through coculture under aerobic or anaerobic conditions. Under aerobic or anaerobic conditions, stimulation of the DC line with all live commensal bacteria examined, except the probiotic Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus), significantly increased the geometric mean fluorescent intensity (MFI) of marker proteins (HLA-ABC, HLA-DR, CD80, CD86, CD83, or CCR7) on the DC surface. In particular, both Fusobacterium nucleatum (F. nucleatum) and Escherichia coli (E. coli) significantly increased the expression of DC-associated molecules, except for CD83 under both aerobic and anaerobic conditions. The DC line stimulated with Fusobacterium varium (F. varium) significantly increased only CD80, HLA-ABC, and HLA-DR expression under anaerobic conditions. Moreover, differences in the levels of proinflammatory cytokines, such as IL-6, IL-8, and TNF-α, were detected in the DC line stimulated by all live commensal bacteria under either aerobic or anaerobic conditions. Under aerobic conditions, the DC line stimulated with E. coli produced significantly more IL-6, IL-8, and TNF-α than did the cells stimulated with any of the bacteria examined. When E. coli were used to stimulate the DC line under anaerobic conditions, TNF-α was predominantly produced compared to stimulation with any other bacteria. Compared to the DC line stimulated with any other bacteria, the cells stimulated with F. nucleatum showed significantly increased production of IL-6, IL-8 and TNF-α only under anaerobic conditions. In particular, E. coli, F. nucleatum, and F. varium strongly stimulated the DC line, resulting in significantly increased expression of surface molecules associated with DCs and production of inflammatory cytokines.

Soil aeration is a crucial factor that regulates crop residue decomposition, and the chemical composition of decomposing crop residues may change the forms and availability of soil nutrients, such as N and P. However, to date, differences in the chemical composition of crop straw residues after incorporation into soil and during its decomposition under anaerobic vs. aerobic conditions have not been well documented. The objective of the present study was to assess changes in the C-containing functional groups of wheat straw residue during its decomposition in anaerobic and aerobic environments. A 12-month incubation experiment was carried out to investigate the temporal variations of mass, carbon, and nitrogen loss, as well as changes in the chemical composition of wheat (Triticum aestivum L) straw residues under anaerobic and aerobic conditions by measuring C-containing functional groups using solid state nuclear magnetic resonance (NMR) spectroscopy. The residual mass, carbon content, and nitrogen content of the straw residue sharply declined during the initial 3 months, and then slowly decreased during the last incubation period from 3 to 12 months. The decomposition rate constant (k) for mass loss under aerobic conditions (0.022 d-1) was higher than that under anaerobic conditions (0.014 d-1). The residual mass percentage of cellulose and hemicellulose in the wheat straw gradually declined, whereas that of lignin gradually increased during the entire 12-month incubation period. The NMR spectra of C-containing functional groups in the decomposing straw under both aerobic and anaerobic conditions were similar at the beginning of the incubation as well as at 1 month, 6 months, and 12 months. The main alterations in C-containing functional groups during the decomposition of wheat straw were a decrease in the relative abundances of O-alkyl C and an increase in the relative abundances of alkyl C, aromatic C and COO/N-C = O functional groups. The NMR signals of alkyl C and aromatic C in decomposing wheat straw residues under anaerobic condition were higher than those under aerobic conditions. The higher mass percentages of lignin and the higher signals of aromatic C and alkyl C functional groups in decomposing wheat residues under anaerobic conditions than under aerobic conditions were due to the slower decomposition rates of aryl C and alkyl C in wheat straw residues under anaerobic conditions.

Antimicrobial treatments result in the host’s enteric bacteria being exposed to the antimicrobials. Pharmacodynamic models can describe how this exposure affects the enteric bacteria and their antimicrobial resistance. The models utilize measurements of bacterial antimicrobial susceptibility traditionally obtained in vitro in aerobic conditions. However, in vivo enteric bacteria are exposed to antimicrobials in anaerobic conditions of the lower intestine. Some of enteric bacteria of food animals are potential foodborne pathogens, e.g., Gram-negative bacilli Escherichia coli and Salmonella enterica. These are facultative anaerobes; their physiology and growth rates change in anaerobic conditions. We hypothesized that their antimicrobial susceptibility also changes, and evaluated differences in the susceptibility in aerobic vs. anaerobic conditions of generic E. coli and Salmonella enterica of diverse serovars isolated from cattle feces. Susceptibility of an isolate was evaluated as its minimum inhibitory concentration (MIC) measured by E-Test® following 24 hours of adaptation to the conditions on Mueller-Hinton agar, and on a more complex tryptic soy agar with 5% sheep blood (BAP) media. We considered all major antimicrobial drug classes used in the U.S. to treat cattle: β-lactams (specifically, ampicillin and ceftriaxone E-Test®), aminoglycosides (gentamicin and kanamycin), fluoroquinolones (enrofloxacin), classical macrolides (erythromycin), azalides (azithromycin), sulfanomides (sulfamethoxazole/trimethoprim), and tetracyclines (tetracycline). Statistical analyses were conducted for the isolates (n≥30) interpreted as susceptible to the antimicrobials based on the clinical breakpoint interpretation for human infection. Bacterial susceptibility to every antimicrobial tested was statistically significantly different in anaerobic vs. aerobic conditions on both media, except for no difference in susceptibility to ceftriaxone on BAP agar. A satellite experiment suggested that during first days in anaerobic conditions the susceptibility changes with time. The results demonstrate that assessing effects of antimicrobial treatments on resistance in the host’s enteric bacteria that are Gram negative facultative Anaerobe Bacilli requires data on the bacterial antimicrobial susceptibility in the conditions resembling those in the intestine.

<p>Soil enzymes produced by microorganisms and plants are very sensitive to the variations in microclimate, e.g. aeration, and respond quickly to the induced changes. The majority of the enzyme assays are conducted under normal (temperature and air) conditions irrespectively of the origin of the environmental samples. However, it remains unclear how conditions of assays may affect results in anaerobic systems. In the present study, we have clarified this key gap in current methods by measuring the kinetics of phosphatase, β-glucosidase, and leucine aminopeptidase in paddy soil under aerobic and anaerobic conditions by means of a glovebox. Specifically, we quantified V<sub>max</sub> and K<sub>m</sub> in soil from three compartments in a rhizobox (top bulk (2-5 cm), rhizosphere, and bottom bulk (15-18 cm)) during rice growth. We demonstrate that the activities of three tested enzymes were significantly lower under aerobic conditions compared to anaerobic conditions at three consecutive dates of rice growth. Lower V<sub>max</sub> values for phosphatase in top bulk soil and rhizosphere soil and β-glucosidase in top bulk soil, rhizosphere soil, and bottom bulk soil confirmed that aerobic conditions limited enzyme activities. For leucine aminopeptidase, although the difference in V<sub>max</sub> values between anaerobic and aerobic conditions was not significant, the values always increased under anaerobic conditions compared to aerobic conditions. Compared with anaerobic conditions, the K<sub>m</sub> values for phosphatase under aerobic conditions decreased by 10.11-22.78%. The maximum difference in the K<sub>m</sub> values for β-glucosidase and leucine aminopeptidase between aerobic and anaerobic conditions was 30.93% and 40.53%, respectively. We conclude that enzyme activities of samples taken from the anaerobic or low-redox environment have to be assayed under anoxic conditions to avoid 10-40% underestimation (for V<sub>max</sub>) due to suppression by oxygen.</p>

Fusarium species cause a broad spectrum of infections including superficial infections in healthy people or disseminated infections in immunocompromised patients. Many of these infections have been associated with proteases secreted by fungi to degrade keratin, an important component of the skin and other tissues. Ischemia and abscess are complications associated to the lack of oxygen in severe mycosis caused by Fusarium. However studies of protein degradation by fungi have been done only in aerobic condition. In this study we hypothesized that protease production would be greater in anaerobic than in aerobic condition. 14 Fusarium isolated from environmental samples were grown in Gelatin Media enriched with sodium nitrate to compare their ability to degrade proteins in anaerobic vs. aerobic conditions. Also antibiotic susceptibility was tested using Fluconazole, Itraconazole and Myconazole in aerobic and anaerobic conditions. All fungi tested showed higher Hydrolysis Capacity Index under anaerobic conditions. In aerobic conditions almost all the fungi tested showed similar colony sizes and halo of protein degradation. On other hand, under anaerobic conditions smallest colony sizes exhibited greater halos of protein degradation. Similarly, all fungi tested were more susceptible to antibiotics in anaerobic conditions too. This study showed high protein degradation in anaerobic conditions. Usually fungal contribution to degradation is ignored due to their low presence in environmental or clinical samples under anaerobic conditions. Our results suggest that Fusarium population could have a role or an impact in anaerobic environments such as ischemia or abscess where protein degradation takes place. Future works includes identification of proteins secreted under anaerobic conditions.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Erv1 is a flavin-dependent sulfhydryl oxidase in the mitochondrial intermembrane space (IMS) that functions in the import of cysteine-rich proteins. Redox titrations of recombinant Erv1 showed that it contains three distinct couples with midpoint potentials of -320, -215, and -150 mV. Like all redox-active enzymes, Erv1 requires one or more electron acceptors. We have generated strains with erv1 conditional alleles and employed biochemical and genetic strategies to facilitate identifying redox pathways involving Erv1. Here, we report that Erv1 forms a 1:1 complex with cytochrome c and a reduced Erv1 can transfer electrons directly to the ferric form of the cytochrome. Erv1 also utilized molecular oxygen as an electron acceptor to generate hydrogen peroxide, which is subsequently reduced to water by cytochrome c peroxidase (Ccp1). Oxidized Ccp1 was in turn reduced by the Erv1-reduced cytochrome c. By coupling these pathways, cytochrome c and Ccp1 function efficiently as Erv1-dependent electron acceptors. Thus, we propose that Erv1 utilizes diverse pathways for electron shuttling in the IMS.

The Escherichia coli fumarate-nitrate reduction regulator (FNR) protein is the paradigm for bacterial O2-sensing transcription factors. However, unlike E. coli, some bacterial species possess multiple FNR proteins that presumably have evolved to fulfill distinct roles. Here, three FNR proteins (ANR, PP_3233, and PP_3287) from a single bacterial species, Pseudomonas putida KT2440, have been analyzed. Under anaerobic conditions, all three proteins had spectral properties resembling those of [4Fe-4S] proteins. The reactivity of the ANR [4Fe-4S] cluster with O2 was similar to that of E. coli FNR, and during conversion to the apo-protein, via a [2Fe-2S] intermediate, cluster sulfur was retained. Like ANR, reconstituted PP_3233 and PP_3287 were converted to [2Fe-2S] forms when exposed to O2, but their [4Fe-4S] clusters reacted more slowly. Transcription from an FNR-dependent promoter with a consensus FNR-binding site in P. putida and E. coli strains expressing only one FNR protein was consistent with the in vitro responses to O2. Taken together, the experimental results suggest that the local environments of the iron-sulfur clusters in the different P. putida FNR proteins influence their reactivity with O2, such that ANR resembles E. coli FNR and is highly responsive to low concentrations of O2, whereas PP_3233 and PP_3287 have evolved to be less sensitive to O2.

Measuring the nitrogen isotope compositions (δ15N) of nitric oxide (NO) from different sources helps to quantify the relative contributions of atmospheric NOx. Soil is one of the most important sources of atmospheric NOx, but only limited measurements on the δ15N of soil‐emitted NO exist, hampering our ability to partition sources to air pollution. Here we conducted soil incubations to measure the δ15N‐NO under defined aerobic or anaerobic conditions, favoring either nitrification or denitrification. Soils were collected from seven sites spanning three ecosystems in northern China (two agricultural, two forest, and three grassland sites). We found that the δ15N‐NO and their associated N isotope fractionations were significantly different between anaerobic and aerobic conditions in seven soils. Under aerobic condition, the δ15N‐NO ranged from −62‰ to −50‰ (averaged −56 ± 4‰), being significantly more negative (by 23‰) than those under anaerobic condition (−45‰ to −23‰, averaged −33 ± 7‰). The apparent N isotope fractionation for NO production under aerobic condition (15εaerobic = 61 ± 3‰) was significantly higher (by 26‰) than under anaerobic condition (15εanaerobic = 35 ± 6‰), with a small variability among ecosystem types. Our study demonstrates that the δ15N‐NO from different soils are very different from fuel combustions (mainly from 0‰ to +20‰), supporting that measuring 15N is a useful tool to partition the contributions of soil NO to atmospheric NOx. Our results also imply δ15N‐NO produced by nitrification and denitrification distinctly different, as these two processes are dominant processes producing NO under aerobic and anaerobic conditions, respectively.

The Effects of Kinetin and Gibberellin on the Germination of Dehusked Seeds of Indica and Japonica Rice (Oryza sativaL.) under Anaerobic and Aerobic Conditions

Antimicrobial peptides (AMPs) can cause lysis of target bacteria by directly inserting themselves into the lipid bilayer. This killing mechanism confounds the identification of the intracellular targets of AMPs. To circumvent this, we used a shuttle vector containing the inducible expression of a human cathelicidin-related AMP, LL-37, to examine its effect on Escherichia coli TOP10 under aerobic and anaerobic growth conditions. Induction of LL-37 caused growth inhibition and alteration in cell morphology to a filamentous phenotype. Further examination of the E. coli cell division protein FtsZ revealed that LL-37 did not interact with FtsZ. Moreover, intracellular expression of LL-37 results in the enhanced production of reactive oxygen species (ROS), causing lethal membrane depolarization under aerobic conditions. Additionally, the membrane permeability was increased after intracellular expression of LL37 under both aerobic and anaerobic conditions. Transcriptomic analysis revealed that intracellular LL-37 mainly affected the expression of genes related to energy production and carbohydrate metabolism. More specifically, genes related to oxidative phosphorylation under both aerobic and anaerobic growth conditions were affected. Collectively, our current study demonstrates that intracellular expression of LL-37 in E. coli can inhibit growth under aerobic and anaerobic conditions. While we confirmed that the generation of ROS is a bactericidal mechanism for LL-37 under aerobic growth conditions, we also found that the intracellular accumulation of cationic LL-37 influences the redox and ion status of the cells under both growth conditions. These data suggest that there is a new AMP-mediated bacterial killing mechanism that targets energy metabolism.

Despite many prior studies on microbial response to oxidative stress, our understanding of microbial tolerance against oxidative stress is currently limited to aerobic conditions, and few engineering strategies have been devised to resolve toxicity issues of oxidative stress under anaerobic conditions. Since biological processes, such as anaerobic fermentation, are frequently hampered by toxicity arising from oxidative stress, increased microbial tolerance against oxidative stress improves the overall productivity and yield of biological processes. Here, we show a systems-level analysis of oxidative stress response of Escherichia coli under anaerobic conditions, and present an engineering strategy to improve oxidative stress tolerance. First, we identified essential cellular mechanisms and regulatory factors underlying oxidative stress response under anaerobic conditions using a transcriptome analysis. In particular, we showed that nitrogen metabolisms and respiratory pathways were differentially regulated in response to oxidative stress under anaerobic and aerobic conditions. Further, we demonstrated that among transcription factors with oxidative stress-derived perturbed activity, the deletion of arcA and arcB significantly improved oxidative stress tolerance under aerobic and anaerobic conditions, respectively, whereas fnr was identified as an essential transcription factor for oxidative stress tolerance under anaerobic conditions. Moreover, we showed that oxidative stress increased the intracellular NADH : NAD(+) ratio under aerobic and anaerobic conditions, which indicates a regulatory role of NADH in oxidative stress tolerance. Based on this finding, we demonstrated that increased NADH availability through fdh1 overexpression significantly improved oxidative stress tolerance under aerobic conditions. Our results here provide novel insight into better understanding of cellular mechanisms underlying oxidative stress tolerance under anaerobic conditions, and into developing strain engineering strategies to enhance microbial tolerance against oxidative stress towards improved biological processes.