Microbial catabolic activities are naturally selected by metabolic energy harvest rate

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.     

The mixed substrate concept, applied for microbial syntheses of metabolites

Microbial overproduction of metabolites is a response to suboptimal conditions for growth and multiplication. It is an energy-wasting process in terms of life insofar as a part of energy of the carbon source remains in the metabolite. From an energetic point of view microbial overproduction can be divided into two categories: i) energy-consuming, ii) energy-yielding. The amount of energy required or made available is considered to be responsible for discrepancies between carbon metabolism-determined possible and experimentally obtained yields. Since the expenditure of energy must be provided by oxidation of carbon source more substrate is consumed than required according to the metabolic pathway. In the case of energy-yielding synthesis energy must be discharged. Various possibilities exist. Since metabolic sequences not involved in the synthesis of the proper product are not switched off completely other synthetic processes and even growth can occur. The energy is thus discharged at the expense of substrate. To increase the experimental yield the energy produced or consumed has to be maintained low. This can be achieved by means of substrate mixtures. The synthesis of by-products and growth are difficult to prevent completely. However, growth can be quite desirable since the catalyst is renewed thus making the product synthesis possible.     

Heat evolution of microbial catabolism: effects of monooxygenases.

Heat evolved during microbial oxidation, expressed as a fraction of total energy available from each compound, was increased by monooxygenase participation. It was less for growth substrate catabolites than for their isomers.     

Generation of electric potential difference across the electrodes of the microbial fuel cell in the anaerobic oxidation of substrates by microbial associations

Several microbial associations were obtained from natural and anthropogenic sources. All of the associations grow well on glucose and significantly worse on acetate. We observed 80–95% glucose consumption during 3–5 days of growth. The oxidation of substrates by the cultures generates an electric potential difference between anode and cathode electrodes of a microbial fuel cell (MFC). The value of the potential difference depends on the nature of the association and the substrate and reaches 400–500 mV. The potential difference generation accompanied by a shift to the negative region of the medium redox potential (E _h ) to — (400–500) mV. This indicates H₂ evolution by the association cultures during oxidation of carbohydrates. Artificial redox mediators, such as tetramethyl-p-phenylenediamine, phenazine methosulfate, and benzyl viologen, were able to increase up to 15% the difference in electrical potential across the electrodes of the MFC. It is assumed that an increase in the potential difference across the electrodes induced by the redox mediators is due to their direct involvement in the transfer of electrons from the bacteria in the incubation medium to the MFC anode electrode. The direct measurement of current and potential difference on the electrodes in a short-circuit mode shows that the internal resistance of the MFC is equal to 1 kΩ and the power reaches 5 μW. Undoubtedly, this testifies to the low efficiency developed by the MFE.     

Diversity of the communities of acidophilic chemolithotrophic microorganisms in natural and technogenic ecosystems

The main representatives of acidophilic chemolithotrophs oxidizing sulfide minerals, ferrous iron, elemental sulfur, and reduced sulfur compounds and forming microbial communities in the natural and technogenic ecosystems with low pH values and high concentrations of heavy metal ions are listed. The species and strain diversity of the communities and environmental factors affecting their composition (temperature, pH value, energy substrate, mineralogical composition of sulfide ore concentrates, the presence of organic substances, and level of aeration) are analyzed. Involvement of mobile genetic elements (IS elements and plasmids) in the structural changes of the chromosomal DNA in the course of switching microbial metabolism to the oxidation of new energy substrates or under increased concentrations of metal ions is shown to be a probable mechanism responsible for the intraspecific genetic heterogeneity of the populations. Importance of determination of the dominant strains of different microbial species in the communities and of their physiological peculiarities for stabilization, optimization, and enhancement of efficiency of biotechnological processes for sulfide mineral oxidation is stressed.     

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki''s Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.     

Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction

Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell to global scales. Energy use efficiency (EUE) is at least as important as the CUE because (i) microorganisms use organic C mainly as an energy source and not as elemental C per se, and (ii) microbial growth and maintenance are limited by energy, but not by C as a structural element. We conceptualize and review the importance of EUE by soil microorganisms and focus on (i) the energy content in organic compounds depending on the nominal oxidation state of carbon (NOSC), (ii) approaches to assess EUE, (iii) similarities and differences between CUE and EUE, and (iv) discuss mechanisms responsible for lower EUE compared to CUE. The energy content per C atom (enthalpy of combustion, the total energy stored in a compound) in organic compounds is very closely (R² = 0.98) positively related to NOSC and increases by 108 kJ mol⁻¹ C per one NOSC unit. For the first time we assessed the NOSC of microbial biomass in soil (−0.52) and calculated the corresponding energy content of −510 kJ mol⁻¹ C. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The mean microbial EUE (0.32–0.35) is 18% lower than CUE (0.41) using glucose as a substrate. This definitely indicates that microbial growth is limited by energy relative to C. Based on the comparison of a broad range of processes of C and energy utilization for cell growth and maintenance, as well as database of experimental CUE from various compounds, we clearly explained five mechanisms and main factors why EUE is lower than CUE. The two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.     

Primary oxidation of organic matter in the soil

Summary The course of respiration rate during glucose decomposition in a soil sample was studied. The whole process of oxidation (mineralization) is divided into two principal parts: the primary oxidation which occurs while the substrate is still present and the secondary oxidation after the disappearance of the substrate. The primary oxidation brought about by two different components: the oxidative component represents the sum of enzyme activity present originally in the soil sample, and the assimilative component is built up during the process by synthesis of microbial enzymes. The size of the oxidative component is correlated with the biological potency of soil. Sometimes, an intermediary stage can be observed at the beginning of the secondary oxidation. A method is given for enumeration of the proportions of the two components involved in primary oxidation. The biochemical and pedological meaning of these data is discussed.     

Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities

Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.     

分子生态网络揭示冶金微生物对能源底物的响应

通过分析不同铁硫比的能源底物驯化下冶金微生物群落的演替过程,基于分子生态网络揭示冶金微生物对能源底物的响应特征。对富铁少硫、富硫少铁条件下不同驯化批次的微生物样本进行高通量测序,分析物种组成,比较冶金微生物群落的α多样性和β多样性,并构建分子生态网络,探究驯化过程微生物之间的相互作用关系。鉴定关键物种,分析冶金微生物群落对能源底物的响应。研究发现在基于不同能源底物驯化过程中,富铁少硫群落的优势物种为嗜酸氧化亚铁硫杆菌Acidithiobacillus ferrooxidans和铁氧化嗜酸硫杆菌A. ferriphilus;而富硫少铁群落经过3个批次的驯化,氧化硫硫杆菌A. thiooxidans占比高达90%。α、β多样性分析结果表明,富硫少铁能源底物驯化过程使冶金微生物群落多样性降低,且随着驯化批次的增加群落组成发生显著变化。分子生态网络分析显示关键物种均为低丰度稀有物种,富硫少铁条件下菌种间具有更紧密的互作共生关系,群落更加稳定。通过该驯化实验,明确了不同能源底物对冶金微生物群落的影响。采用富硫少铁能源底物驯化冶金微生物,使冶金微生物群落更加稳定,有助于优势物种高效发挥铁、硫氧化功能,促进硫化矿物的氧化溶解,为生物冶金工业育种微生物群落的定向驯化提供理论基础。     

Estimating changes of isotopic fractionation based on chemical kinetics and microbial dynamics during anaerobic methane oxidation: apparent zero- and first-order kinetics at high and low initial methane concentrations

Changes in natural isotopic composition may be used to reveal metabolic pathways of substrate transformation by microbial communities (Vavilin in Ecol Model 240:84–92, 2012b). Anaerobic oxidation of methane (AOM) by sulfate has been described using a mathematical model based on chemical kinetics, microbial dynamics and equations for ¹³C isotope accumulation in products as well as their redistribution between substrate and products. Experimental data for two batch cultures that originated from microbial mats covering methane seep chimneys in the Black Sea, previously obtained by Seifert et al. (Org Geochem 37:1411–1419, 2006) and Holler et al. (Env Microbiol Reports 1(5):370–376, 2009), were used to model AOM. During long-time incubation, changes of isotope signatures in CH₄ showed that in the Seifert et al. batch tests (low methane concentration), in contrast to the Holler et al. batch tests (high methane concentration), methane production occurred along with methane oxidation. In accordance with the model, apparent zero and first-order kinetics of methane oxidation were valid for the Holler et al. and Seifert et al. batch tests, respectively. The observed change of $ \delta {}^{13}{\text{CH}}_{4} $ was explained by microbial kinetics reflecting that the rate is lower for heavy substrate microbial utilization when compared to light substrate microbial utilization. The model showed that small amounts of methanogenesis will change the carbon isotopic composition of methane because biogenic methane has a distinct isotopic composition and due to the large difference between the maximum specific rates of methane oxidation and production. The estimated biomass doubling time of methane-oxidizers for high and low methane concentration was 408/126 days and 4640/1160 days, respectively, depending on the value of the half-saturation constant K _S (5 and 20 mM).     

“吃”砒霜的细菌--解析微生物的砷代谢

研究发现一些微生物可以利用剧毒的类金属砷(As)为自身生长获取能量甚至用砷代替磷维持生长。本文综合分析了近期的研究进展,从以下6方面解析微生物多重的砷代谢产能机制:(1)化能无机自养As(Ⅲ)氧化供能;(2)有机异养型As(Ⅲ)氧化供能;(3)呼吸性As(Ⅴ)还原供能;(4)As(Ⅲ)氧化偶联的光合作用;(5)As(Ⅲ)氧化、As(Ⅴ)、还原As(Ⅲ)氧化偶联的光合作用之间的关联;(6)As(Ⅴ)代替磷维持细菌生长。阐明微生物利用砷的机理在生命起源、生命多样性、进化、地球化学循环及污染治理等方面都具有重要价值。     

Rock structure drives the taxonomic and functional diversity of endolithic microbial communities in extreme environments

Endolithic (rock-dwelling) microbial communities are ubiquitous in hyper-arid deserts around the world and the last resort for life under extreme aridity. These communities are excellent models to explore biotic and abiotic drivers of diversity because they are of low complexity. Using high-throughput amplicon and metagenome sequencing, combined with X-ray computed tomography, we investigated how water availability and substrate architecture modulated the taxonomic and functional composition of gypsum endolithic communities in the Atacama Desert, Chile. We found that communities inhabiting gypsum rocks with a more fragmented substrate architecture had higher taxonomic and functional diversity, despite having less water available. This effect was tightly linked with community connectedness and likely the result of niche differentiation. Gypsum communities were functionally similar, yet adapted to their unique micro-habitats by modulating their carbon and energy acquisition strategies and their growth modalities. Reconstructed population genomes showed that these endolithic microbial populations encoded potential pathways for anoxygenic phototrophy and atmospheric hydrogen oxidation as supplemental energy sources.     

Use of gamma-irradiation of soil for analyzing the state of microbial coeneses]

Increasing doses of gamma-irradiation eliminate some physiological and ecologo-trophical groups from microbial cenoses in soil. Soil fungi are least resistant to the action of gamma-irradiation (do not grow on agarized soil (AS) at a dose of 0.5 Mrad). Actinomycetes are more resistant (do not grow on AS at a dose of 0.75 Mrad). Bacteria are most resistant to irradiation. Asporogenous bacteria do not grow on agarized soil at a dose of 1.25 Mrad. Sporogenous bacteria survive at higher doses (1.75 Mrad). The method of gamma-irradiation permits to accomplish differential analysis of ecological groups of soil microflora and experimental synthesis of microbial associations. The effect of gamma-irradiation on soil enzymes is weak compared with autoclaving. gamma-Irradiated soils may serve as a substrate for model experiments during analysis of microbial associations.     

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic ‘bins'' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.     

Characterization of Thermophilic Consortia from Two Souring Oil Reservoirs

The microbial consortia from produced water at two different oil fields in Alaska (Kuparuk) and the North Sea (Ninian) were investigated for sulfate-reducing and methanogenic activity over a range of temperatures and for a variety of substrates. The consortia were sampled on site, and samples were either incubated on site at 60(deg)C with various substrates or frozen for later incubation and analyses. Temperature influenced the rates of sulfate reduction, hydrogen sulfide production, and substrate oxidation, as well as the cell morphology. The highest rates of sulfate reduction and substrate oxidation were found between 50 and 60(deg)C. Formate and n-butyrate were the most favorable electron donors at any tested temperature. Acetate was utilized at 35(deg)C but not at 50 or 70(deg)C and was produced at 60(deg)C. This indicates that the high levels of acetate found in produced water from souring oil formations are due mainly to an incomplete oxidation of volatile fatty acids to acetate. The cell size distribution of the microbial consortium indicated a nonuniform microbial composition in the original sample from the Kuparuk field. At different temperatures, different microbial morphologies and physiologies were observed. Methane-producing activity at thermophilic temperatures (60(deg)C) was found only for the Kuparuk consortium when hydrogen and carbon dioxide were present. No methane production from acetate was observed. Suppression of methanogenic activity in the presence of sulfate indicated a competition with sulfate-reducing bacteria for hydrogen.     

Energy deficit without reducing dietary carbohydrate alters resting carbohydrate oxidation and fatty acid availability.

Reduced carbohydrate (CHO) availability after exercise has a potent influence on the regulation of substrate metabolism, but little is known about the impact of fat availability and/or energy deficit on fuel metabolism when dietary CHO availability is not reduced. The purpose of this study was to determine the influence of a postexercise energy deficit, independent of CHO availability, on plasma substrate concentrations and substrate oxidation. Seven moderately trained men (peak oxygen uptake: 56 +/- 2 ml.kg(-1).min(-1)) performed exhaustive cycling exercise on two separate occasions. The two trials differed only by the meals ingested after exercise: 1) a high-fat diet designed to maintain energy balance or 2) a low-fat diet designed to elicit energy deficit. The CHO and protein contents of the diets were identical. The next morning, we measured plasma substrate and insulin concentrations and CHO oxidation, and we obtained muscle biopsies from the vastus lateralis for measurement of pyruvate dehydrogenase kinase (PDK)-2 and PDK-4 mRNA expression by using RT-PCR. Despite identical blood glucose (5.0 +/- 0.1 and 4.9 +/- 0.1 mM) and insulin (7.9 +/- 1.1 and 8.4 +/- 0.9 microU/ml) concentrations, plasma fatty acid and glycerol concentrations were elevated three- to fourfold during energy deficit compared with energy balance and CHO oxidation was 40% lower (P < 0.01) the morning after energy deficit compared with energy balance (328 +/- 69 and 565 +/- 89 micromol/min). The lower CHO oxidation was accompanied by a 7.3 +/- 2.5-fold increase in PDK-4 mRNA expression after energy deficit (P < 0.05), whereas PDK-2 mRNA was similar between the trials. In conclusion, energy deficit increases fatty acid availability, increases PDK-4 mRNA expression, and suppresses CHO oxidation even when dietary CHO content is not reduced.     

Analysis of Factors Affecting the Accuracy, Reproducibility, and Interpretation of Microbial Community Carbon Source Utilization Patterns

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microtiter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal-components analysis (PCA), and model communities with different compositions were clearly separated on the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.