Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity

Microbial thermogenesis is dependent on ATP concentrations and the protein kinases ArcB, GlnL, and YccC

Organisms necessarily release heat energy in their pursuit of survival. This process is known as cellular thermogenesis and is implicated in many processes from cancer metabolism to spontaneous farm fires. However, the molecular basis for this fundamental phenomenon is yet to be elucidated. Here, we show that the major players involved in the cellular thermogenesis of Escherichia coli are the protein kinases ArcB, GlnL, and YccC. We also reveal the substrate-level control of adenosine triphosphate (ATP)-driven autophosphorylation that governs cellular thermogenesis. Specifically, through live cell microcalorimetry, we find these regulatory proteins, when knocked out in a model E. coli strain, dysregulate cellular thermogenesis. This dysregulation can be seen in an average 25% or greater increase in heat output by these cells. We also discover that both heat output and intracellular ATP levels are maximal during the late log phase of growth. Additionally, we show that microbial thermogenesis can be engineered through overexpressing glnL. Our results demonstrate a correlation between ATP concentrations in the cell and a cell's ability to generate excess heat. We expect this work to be the foundation for engineering thermogenically tuned organisms for a variety of applications.

Cadmium-Tolerant Bacteria in Cacao Farms from Antioquia, Colombia: Isolation, Characterization and Potential Use to Mitigate Cadmium Contamination

Bioremediation of farm soil is a technique that merits in-depth research. There are few studies related to the use of bioremediation to reduce cadmium (Cd) availability in soils used for cacao production. This study investigates (1) field bioprospection and strain characterization using techniques including isothermal microcalorimetry to select a group of cadmium-tolerant bacteria (CdtB) for potential use as bioremediators of cacao soils and (2) the application of bacterial inoculum to compare the immobilization of Cd under field conditions. Bioprospection was carried out in four cacao farms from the Antioquia district in Colombia. Culturable CdtB strains were isolated using CdCl2 as a Cd source and identified using molecular techniques. The metabolic characterization of Cd immobilization was carried out using isothermal microcalorimetry with CdCl2 amendments. Five cadmium-tolerant bacteria were isolated and characterized as Bacillus spp. The strain CdtB14 showed better growth and Cd immobilization ability (estimated through heat ratios) than any strain isolated thus far, suggesting potential for future use in bioproduct development. Furthermore, the application of two previously characterized CdtB strains with zeolite powder was performed in the same farms where the bioprospection process was carried out. The application of the preformulated inoculum resulted in a decrease of 0.30 + 0.1 mg kg−1 of soil Cd in two out of the four assessed farms. The field results are preliminary and require data on the change in Cd in cacao beans to understand what this result means for Cd mitigation. This study is the first to combine bioprospecting and the performance of CdtB in laboratory and field experiments in cacao farms and shows the potential of bioremediation to mitigate Cd contamination in cacao.

Cadmium-tolerant bacteria: current trends and applications in agriculture

Cadmium (Cd) is considered a toxic heavy metal; nevertheless, its toxicity fluctuates for different organisms. Cadmium-tolerant bacteria (CdtB) are diverse and non-phylogenetically related. Because of their ecological importance these bacteria become particularly relevant when pollution occurs and where human health is impacted. The aim of this review is to show the significance, culturable diversity, metabolic detoxification mechanisms of CdtB and their current uses in several bioremediation processes applied to agricultural soils. Further discussion addressed the technological devices and the possible advantages of genetically modified CdtB for diagnostic purposes in the future.

A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology

Viability and metabolic assays are commonly used as proxies to assess the overall metabolism of microorganisms. The variety of these assays combined with little information provided by some assay kits or online protocols often leads to mistakes or poor interpretation of the results. In addition, the use of some of these assays is restricted to simple systems (mostly pure cultures), and care must be taken in their application to environmental samples. In this review, the necessary data are compiled to understand the reactions or measurements performed in many of the assays commonly used in various aspects of microbiology. Also, their relationships to each other, as metabolism links many of these assays, resulting in correlations between measured values and parameters, are discussed. Finally, the limitations of these assays are discussed.

Microcalorimetry and enzyme activity to determine the effect of nickel and sodium butyl xanthate on soil microbial community

In non-ferrous metal tailings, combined pollution in the surrounding soil is caused by heavy metals and flotation chemicals. The combined effects of nickel (Ni) and its primary ore processing collector, sodium butyl xanthate (SBX), on soil microbial activity were investigated following the fluorescein diacetate hydrolase (FDA) and sucrase (SA) activities, and isothermal microcalorimetry during 60 days. FDA and SA activities as well as overall soil microbial activity were significantly affected by Ni, SBX and Ni/SBX mixture. The inhibition rate (I) of the growth rate constant (k) being higher with the Ni/SBX mixture than with SBX alone during the experiment. The growth rate constant (k) was positively correlated (p < 0.05 or p < 0.01) with enzyme activities (FDA and SA) indicating that k represented a valuable proxy to evaluate the toxic effect of metals and flotation reagents on soil microorganisms. Thus, microcalorimetry was a useful method to characterize soil microbial communities.

Exploring an in situ LED-illuminated isothermal micro-calorimetric method to investigating the thermodynamic behavior of Chlorella vulgaris during CO2 bio-fixation

Much endeavor has been dispensed recently to evaluate the potential of CO₂ mitigation by microalgae. We introduce an alternative, novel, LED-illumination isothermal microcalorimetric method to assess the thermodynamic behaviors of microalgae for better understanding of their carbon sequestration capacity. Microalgae thermodynamic behaviors were recorded as power-time curves, and their indices such as total heat evolution (Q_T), maximum power output (P_max) and heat generated by per algae cell (J_N/Q) were obtained. The values for highest (74.80 g L^-1) and control sample (0.00 g L^-1) of Q_T, P_max and J_N/Q were 20.85 and 2.32 J; 252.17 and 57.67 μW; 7.91 × ^-06 and 8.80 × ^-07 J cell^-1, respectively. According to the values of Q_T, a general order to promote the CO₂ sequestration was found at 74.8 g L^-1 > 29.92 g L^-1 > 14.96 g L^-1 > 7.48 g L^-1 > 0 g L^-1 of C sources, which directly corresponded to carbon availability in the growth medium. Chlorella vulgaris GIEC-179 showed the highest peak P_max at 74.8 g L^-1 concentration which was directly transformed to their biomass during bio-fixation of CO₂ process. This study is applicable for better understanding of CO₂ fixation performance of algae.

Toxicity of nickel to soil microbial community with and without the presence of its mineral collectors-a calorimetric approach

The toxicity of nickel and three of its main collectors, sodium isopropyl xanthate (SIPX), sodium ethyl xanthate (SEX), and potassium ethyl xanthate (PEX) to soil microbial activity, was analyzed, individually and as a binary combination of nickel and each of the collectors. The investigation was performed through the microcalorimetric analysis method. For the single chemicals, all power-time curves exhibited lag, exponential, stationary, and death phases of microbial growth. Different parameters exhibited a significant adverse effect of the analyzed chemicals on soil microbial activity, with a positive relationship between the inhibitory ratio and the chemical dose (p < 0.05 or p < 0.01). A peak power reduction level of 24.23% was noted for 50 μg g^-1 soil in the case of Ni while for the mineral collectors, only 5 μg g^-1 soil and 50 μg g^-1 soil induced a peak power reduction level of over 35 and 50%, respectively, in general. The inhibitory ratio ranged in the following order: PEX > SEX > SIPX > Ni. Similar behavior was observed with the mixture toxicity whose inhibitory ratio substantially decreased (maximum decrease of 38.35%) and slightly increased (maximum increase of 15.34%), in comparison with the single toxicity of mineral collectors and nickel, respectively. The inhibitory ratio of the mixture toxicity was positively correlated (p < 0.05 or p < 0.01) with the total dose of the mixture. In general, the lesser and higher toxic effects are those of mixtures containing SIPX and PEX, respectively.

Toxic effect of two kinds of mineral collectors on soil microbial richness and activity: analysis by microcalorimetry, microbial count, and enzyme activity assay

Flotation reagents are hugely and increasingly used in mining and other industrial and economic activities from which an important part is discharged into the environment. China could be the most affected country by the resulting pollution. However, their ecotoxicological dimension is still less addressed and understood. This study aimed to analyze the toxic effect of sodium isobutyl xanthate (SIBX) and sodium isopropyl xanthate (SIPX) to soil microbial richness and activity and to make a comparison between the two compounds in regard to their effects on soil microbial and enzymes activities. Different methods, including microcalorimetry, viable cell counts, cell density, and catalase and fluorescein diacetate (FDA) hydrololase activities measurement, were applied. The two chemicals exhibited a significant inhibitory effect (P < 0.05 or P < 0.01) to all parameters, SIPX being more adverse than SIBX. As the doses of SIBX and SIPX increased from 5 to 300 μg g^-1 soil, their inhibitory ratio ranged from 4.84 to 45.16 % and from 16.13 to 69.68 %, respectively. All parameters fluctuated with the incubation time (10-day period). FDA hydrolysis was more directly affected but was relatively more resilient than catalase activity. Potential changes of those chemicals in the experimental media and complementarity between experimental techniques were justified.

Development of a flow system for studying biofilm formation on medical devices with microcalorimetry

Isothermal microcalorimetry (IMC) is particularly suited to the study of microbiological samples in complex or heterogeneous environments because it does not require optical clarity of the sample and can detect metabolic activity from as few as 10(4) CFU/mL cells. While the use of IMC for studying planktonic cultures is well established, in the clinical environment bacteria are most likely to be present as biofilms. Biofilm prevention and eradication present a number of challenges to designers and users of medical devices and implants, since bacteria in biofilm colonies are usually more resistant to antimicrobial agents. Analytical tools that facilitate investigation of biofilm formation are therefore extremely useful. While it is possible to study pre-prepared biofilms in closed ampoules, better correlation with in vivo behaviour can be achieved using a system in which the bacterial suspension is flowing. Here, we discuss the potential of flow microcalorimetry for studying biofilms and report the development of a simple flow system that can be housed in a microcalorimeter. The use of the flow system is demonstrated with biofilms of Staphylococcus aureus.

Isolation and characterization of oxalotrophic bacteria from tropical soils

The oxalate-carbonate pathway (OCP) is a biogeochemical set of reactions that involves the conversion of atmospheric CO2 fixed by plants into biomass and, after the biological recycling of calcium oxalate by fungi and bacteria, into calcium carbonate in terrestrial environments. Oxalotrophic bacteria are a key element of this process because of their ability to oxidize calcium oxalate. However, the diversity and alternative carbon sources of oxalotrophs participating to this pathway are unknown. Therefore, the aim of this study was to characterize oxalotrophic bacteria in tropical OCP systems from Bolivia, India, and Cameroon. Ninety-five oxalotrophic strains were isolated and identified by sequencing of the 16S rRNA gene. Four genera corresponded to newly reported oxalotrophs (Afipia, Polaromonas, Humihabitans, and Psychrobacillus). Ten strains were selected to perform a more detailed characterization. Kinetic curves and microcalorimetry analyses showed that Variovorax soli C18 has the highest oxalate consumption rate with 0.240 µM h(-1). Moreover, Streptomyces achromogenes A9 displays the highest metabolic plasticity. This study highlights the phylogenetic and physiological diversity of oxalotrophic bacteria in tropical soils under the influence of the oxalate-carbonate pathway.

Oxidation of aquatic pollutants by ferrous-oxalate complexes under dark aerobic conditions

This study evaluates the ability of Fe(II)-oxalate complexes for the generation of OH through oxygen reduction and the oxidative degradation of aquatic pollutants under dark aerobic conditions (i.e., with oxygen but without light). The degradation of 4-chlorophenol (4-CP) was rapid in the mixture of Fe(2+) and oxalate prepared using ultrapure water, but was absent without either Fe(2+) or oxalate. The formation of Fe(II)-oxalate complexes enables two-electron reduction of oxygen to generate H2O2 and subsequent production of OH. The significant inhibition of 4-CP degradation in the presence of H2O2 and OH scavenger confirms such mechanisms. The degradation experiments with varying [Fe(2+)], [oxalate], and initial pH demonstrated that the degradation rate depends on [Fe(II)(Ox)2(2-)], but the degree of degradation is primarily determined by [Fe(II)(Ox)2(2-)]+[Fe(II)(Ox)(0)]. Efficient degradation of diverse aquatic pollutants, especially phenolic pollutants, was observed in the Fe(II)-oxalate complexes system, wherein the oxidation efficacy was primarily correlated with the reaction rate constant between pollutant and OH. The effect of various organic ligands (oxalate, citrate, EDTA, malonate, and acetate) on the degradation kinetics of 4-CP was investigated. The highest efficiency of oxalate for the oxidative degradation is attributed to its high capability to enhance the reducing power and low reactivity with OH.

A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum

Rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.

Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments

The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12 days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soils.

Oxalyl-coenzyme A reduction to glyoxylate is the preferred route of oxalate assimilation in Methylobacterium extorquens AM1

Oxalate catabolism is conducted by phylogenetically diverse organisms, including Methylobacterium extorquens AM1. Here, we investigate the central metabolism of this alphaproteobacterium during growth on oxalate by using proteomics, mutant characterization, and (13)C-labeling experiments. Our results confirm that energy conservation proceeds as previously described for M. extorquens AM1 and other characterized oxalotrophic bacteria via oxalyl-coenzyme A (oxalyl-CoA) decarboxylase and formyl-CoA transferase and subsequent oxidation to carbon dioxide via formate dehydrogenase. However, in contrast to other oxalate-degrading organisms, the assimilation of this carbon compound in M. extorquens AM1 occurs via the operation of a variant of the serine cycle as follows: oxalyl-CoA reduction to glyoxylate and conversion to glycine and its condensation with methylene-tetrahydrofolate derived from formate, resulting in the formation of C3 units. The recently discovered ethylmalonyl-CoA pathway operates during growth on oxalate but is nevertheless dispensable, indicating that oxalyl-CoA reductase is sufficient to provide the glyoxylate required for biosynthesis. Analysis of an oxalyl-CoA synthetase- and oxalyl-CoA-reductase-deficient double mutant revealed an alternative, although less efficient, strategy for oxalate assimilation via one-carbon intermediates. The alternative process consists of formate assimilation via the tetrahydrofolate pathway to fuel the serine cycle, and the ethylmalonyl-CoA pathway is used for glyoxylate regeneration. Our results support the notion that M. extorquens AM1 has a plastic central metabolism featuring multiple assimilation routes for C1 and C2 substrates, which may contribute to the rapid adaptation of this organism to new substrates and the eventual coconsumption of substrates under environmental conditions.