Lithotrophic Bacteria Research Articles

Overcoming Energetic Barriers in Acetogenic C1 Conversion.

Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2 via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.

The role of iron-oxidizing bacteria in biocorrosion: a review

Lithotrophic iron-oxidizing bacteria depend on reduced iron, Fe(II), as their primary energy source, making them natural candidates for growing in association with steel infrastructure and potentially contributing to microbially influenced corrosion (MIC). This review summarizes recent work on the role of iron-oxidizing bacteria (FeOB) in MIC. By virtue of producing complex 3-dimensional biofilms that result from the accumulation of iron-oxides, FeOB may aid in the colonization of steel surfaces by other microbes involved in MIC. Evidence points to a successional pattern occurring whereby FeOB are early colonizers of mild steel (MS), followed by sulfate-reducing bacteria and other microbes, although studies of aged corrosion products indicate that FeOB do establish a long-term presence. There is evidence that only specific clades of FeOB, with unique adaptations for growing on steel surfaces are part of the MIC community. These are discussed in the context of the larger MIC microbiome.

A case in support of implementing innovative bio-processes in the metal mining industry.

The metal mining industry faces many large challenges in future years, among which is the increasing need to process low-grade ores as accessible higher grade ores become depleted. This is against a backdrop of increasing global demands for base and precious metals, and rare earth elements. Typically about 99% of solid material hauled to, and ground at, the land surface currently ends up as waste (rock dumps and mineral tailings). Exposure of these to air and water frequently leads to the formation of acidic, metal-contaminated run-off waters, referred to as acid mine drainage, which constitutes a severe threat to the environment. Formation of acid drainage is a natural phenomenon involving various species of lithotrophic (literally 'rock-eating') bacteria and archaea, which oxidize reduced forms of iron and/or sulfur. However, other microorganisms that reduce inorganic sulfur compounds can essentially reverse this process. These microorganisms can be applied on industrial scale to precipitate metals from industrial mineral leachates and acid mine drainage streams, resulting in a net improvement in metal recovery, while minimizing the amounts of leachable metals to the tailings storage dams. Here, we advocate that more extensive exploitation of microorganisms in metal mining operations could be an important way to green up the industry, reducing environmental risks and improving the efficiency and the economy of metal recovery.

Results of Microbiologic Investigations of Water-Development Works

Results are presented for multiyear field investigations of the effect of microbe colonies on components of water-development works. Concrete, metal, and geologic rocks were studied as component parts of the bed of concrete dams functioning in various climatic zones. The participation of lithotrophic bacteria in processes involving corrosion failure of the metal, concrete, and rock beds of dams is established, and causes of intensification of microbe activity are exposed. The need for monitoring the composition and number of microorganisms-biodestructors is substantiated in the water of a reservoir and observation wells, as well as on the surfaces of structural components of water-development works for monitoring of the safety of the concrete dams.

Effect of Demineralization on Shale Oil Yield by Bioleaching Process of Huadian (China) Oil Shale

In this study, the effect of the mineral matter of Huadian (China) Oil Shale on the conversion of organic carbon of oil shale to shale oil. The bioleaching process is taken in a mixed culture of the lithotrophic bacteria Thiobacillus ferrooxidans(Tf). The aim of bioleaching process was to dissolve the inorganic matters and improve the shale oil yield. A series of temperature-programmed pyrolysis operation was performed with raw and bioleached oil shale to find the best retorting temperature, 500oC is the best temperature to retort the oil shale. The oil shale samples were detected by SEM, DG, Fischer assay test, the results show that the surface structure was significantly different from the raw sample, and the shale oil yield improved from 8.9% to 11.7%.

Communities of neutrophilic iron-oxidizing microorganisms of ferruginous springs of various types and their involvement in fractionation of stable iron isotopes

Abundance and structure of the communities of neutrophilic lithotrophic iron-oxidizing bacteria (FeOB) inhabiting four low-mineralized ferruginous springs of the Marcial Waters Resort (South Karelia, Russia) and the brackish chalybeate spring of the Staraya Russa Resort (Novgorod region, Russia), were investigated, as well as the physicochemical conditions of these environments. In fresh iron-containing precipitates collected near the spring outlets and within the spring-discharge areas, as well as along the spring watercourses, the numbers of unicellular FeOB enumerated on nutrient media ranged from 105 to 107 cells per 1 mL of sediments irrespective of the initial Fe(II) concentration (11–126 mg L−1). In the spring waters and along the spring watercourses inhabited by iron-oxidizing bacteria, the concentration of dissolved oxygen did not exceed 0.05–0.1 mg L−1. Unicellular FeOB were predominant in three springs, while in the springs with relatively low Fe(II) concentrations (11–22 mg L−1), various morphological forms of Gallionella and uncultured forms of the iron-oxidizing bacterium Toxothrix trichogenes prevailed. In the model experiments with the water samples collected in the ferruginous springs and bogs under controlled conditions, the fractionation of stable iron isotopes and the rate of iron oxidation were found to depend on the oxygen regime and, to a lesser extent, on the initial Fe(II) concentration. The maximum enrichment of the iron oxides formed during the simulation experiments with the light 54Fe isotope was observed during bacterial oxidation under microaerobic conditions at O2 concentrations of 0.1–0.3 mg L−1 and in the cultures of iron-oxidizing bacteria. During the abiogenic oxidation of Fe(II), the extent of stable isotope fractionation was 1.5–2 times lower. Enrichment of Fe(III) oxides with the light 54Fe isotope (3- to 5-fold) was considerably lower at high rates of both the biogenic and abiogenic processes of iron oxidation under aerobic conditions; however, it was more intense during the bacterial processes. Comparison of the rates of enrichment of Fe(III) oxides with the light isotope during the model experiments with pure and enrichment cultures of iron-oxidizing bacteria from the sediments of ferruginous springs and bogs revealed that the biogenic factor plays a key role in the oxidation processes of the iron cycle, as well as in the differentiation of the composition of stable iron isotopes in the studied ecosystems.

Lithotrophic Bacterial Leaching of Heavy Metals from Sediments Dredged from the Deûle Canal, France

Lithotrophic bacterial leaching of heavy metals from dredged sediments was studied in semi-pilot scale air-lift bioreactors. Prior to the bioleaching experiments, a physico-chemical characterization of the sediments comprising a sequential extraction study was conducted. The sediments turned out to be highly loaded with heavy metals, and with the exception of managanese, mainly associated to the oxidizable fraction of the sediments and thus strongly linked to the latter. The heavy metals could be classified by decreasing order of mobility as follows: Mn>Zn>Cu>Cd>Pb. The bacterial leaching was found to be strongly dependent on the nature of the mineral substrate. Sulfur gave the best solubilization results in comparison with reduced iron or with a combination of reduced iron and sulfur. In the presence of oxygen, lithotrophic bacteria oxidized sulfur into sulfates and induced an acidification of the sediments. These conditions led to the release of the metals that were tightly linked to the sediments, that is those associated with the sulfides and/or with the organic matter. With sulfur as a substrate, the solubilization percentages varied within 30 days between 72 and 93% of the total sediment content (wt/wt) for cadmium, copper, manganese and zinc. Much lower biosolubilization percentages were obtained in the case of lead because of the poor solubility of lead sulfate.

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia

We investigated bacterial community assemblages and functions down a hill slope contaminated by tailings from a volcanogenic massive sulphide mine in arid Western Australia. Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill. Bacterial community assemblage, characterised by PCR-DGGE fingerprinting, was significantly associated with electrical conductivity (E.C.) (ρ = 0.664; P < 0.01). Analysis of mobile salts showed that E.C. values were driven by ionic S, Zn, Cl and Al. The bacterial community assemblage was directly characterised across an E.C. gradient using an oligonucleotide microarray (PhyloChip). The dominant taxa at the site were Proteobacteria, Actinobacteria and Firmicutes; however, 37 phyla were detected. The most responsive taxa to variation in E.C. was Acidobacteria (negative correlation). Patterns of heterotrophic processes (BioLog analysis) were also best explained by variation in E.C. (ρ = 0.53; P < 0.01), showing a link between primary mineral weathering by lithotrophic bacteria and abiotic processes, and secondary biogeochemical processes by heterotrophic taxa. These data significantly broaden our knowledge of the bacteria present in metallomorphic ecosystems, establish that mobile phase elements are key drivers of community structure, and that primary biogeochemical cycling is directly influencing other geochemical interactions in the samples.

Study of canal sediments contaminated with heavy metals: fungal versus bacterial bioleaching techniques

Filamentous fungi and lithotrophic bacteria were used to leach heavy metals from dredged sediments in semi‐pilot scale air‐lift bioreactors. A preliminary physico‐chemical characterization of the sediments comprising a sequential extraction study revealed their high metallic contamination and a predominant association of the metals with sulphides and organic matter. The mobility of heavy metals from sediments was ranked by decreasing order as follows: Mn > Zn > Cd > Cu > Pb. The conditions that favoured the solubilization of heavy metals by filamentous fungi turned out to be also favourable for the activity of the sediment organotrophic bacteria. The latter produced organic acids under temporary hypoxic conditions and resulted in the solubilization of 77% of manganese, 44% of zinc, 12% of copper, and less than 2% of cadmium or lead. In general, the fungal organotrophic treatments were limited to the relatively mobile metals due to the weak nature of the organic acids produced and to their microbial consumption under limited saccharose conditions. The lithotrophic treatments yielded higher solubilization results than the organotrophic experiments. Sulphur resulted in a faster, and for some metals such as copper and cadmium, in better bioleaching results compared with reduced iron or with a combination of reduced iron and sulphur. The bioleaching percentages varied between 72 and 93% for cadmium, copper, manganese and zinc, except for lead because of the poor solubility of lead sulphate. The sediment’s lithotrophic bacteria acidified the matrix through sulphur oxidation, and leached both loosely and tightly bound metals.

Behavioural and physiological adaptations of the bearded goby, a key fish species of the extreme environment of the northern Benguela upwelling

Nutrient-rich, upwelling marine areas with high productivity often produce sediments dominated by organic-rich mud. Here, intense decay processes create hypoxic conditions with high concentrations of hydrogen sulphide and methane in the muddy surface layers. Such environments are inhospitable to most forms of life and those organisms that can survive in these areas tend to be specialists that cope with anoxic or hypoxic conditions, e.g. sulphide-oxidising bacteria and chemo- lithotrophic bacteria. Surprisingly, during recent acoustic and survey work in the northern Benguela region off the coast of Namibia, it was observed that the bearded goby Sufflogobius bibarbatus spends much of the day on the seabed interacting with the hypoxic and sulphidic mud, making a diel vertical migration (DVM) to spend the night in more oxygenated, but jellyfish-rich waters. We describe a series of experiments that demonstrate physiological and behavioural adaptations that enable the gobies to cope with hypoxia, anoxia and exposure to sulphide for prolonged periods of time. We also observed that the fish burrow directly into the muddy substrate when threatened and that, unlike another fish species common to this area, the horse mackerel Trachurus capensis, the gobies tolerate the presence of jellyfish.

Initial indications of abiotic formation of hydrocarbons in the Rainbow ultramafic hydrothermal system, Mid-Atlantic Ridge

In the presence of water, olivine of ultramafic rock is oxidized during the process referred to as ‘serpentinization’. Water in contact with the olivine is reduced to molecular hydrogen (H2) with the concomitant oxidation of Fe(II). The molecular hydrogen formed may be used as an energy source by lithotrophic bacteria, but may, at high temperature, also be combined with CO2 for the abiotic formation of organic compounds such as hydrocarbons and fatty acids through Fischer–Tropsch type (FTT) synthesis. Our analyses of fluids from the peridotite-hosted Rainbow hydrothermal field on the Mid-Atlantic Ridge indicate de novo synthesis of linear saturated hydrocarbons. The chain length of the hydrocarbons is between 16 and 29 carbon atoms. The discovery of FTT reactions in ultramafic hydrothermal systems on Earth provides an alternative pathway for the formation of early membranes and the origin of life.

Pyrite surfaces after bio-leaching: a mechanism for bio-oxidation

A pyrite mineral surface was exposed to a mixed culture of the lithotrophic bacteria Thiobacillus ferrooxidans (Tf). The surface structure of this sample was compared to surfaces exposed to uninoculated solutions of either sulphuric acid or ferric and ferrous sulfate dissolved in sulfuric acid solution at equivalent concentrations as the inoculated solution. All surfaces were examined using X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). A chemical profile of the surfaces, as a function of depth, was obtained by surface ablation. The colonised surface produced an oxidised phase extending to a depth of more than 4 μm. A carbonaceous phase was not observed within the oxide layer. No oxide layers of significant depth were observed for samples exposed to uninoculated solutions. The importance of the sessile cells in bio-oxidation of pyrite is demonstrated and a qualitative model is proposed.

Stratigraphic and geochemical controls on naturally occurring arsenic in groundwater, eastern Wisconsin, USA

The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface geochemical processes and to develop new approaches to subsurface remediation.

Bacterial and chemical oxidation of pyritic mine tailings at low temperatures

Microbial and chemical sulfide oxidation activity and oxygen consumption was investigated in the active layer of pyritic mine tailings at Nanisivik Mine, located in a permafrost area on Baffin Island in northern Canada. Samples of tailings were collected up to a depth of 60 cm in mid-August 1998 at 4 sites, for which the metabolic activity of sulfur- and iron-oxidizing leaching bacteria besides the chemical pyrite oxidation activity were measured on 39 tailings samples and 7 samples from a natural pyritic site by calorimetry. The tailings of varying age and water content were deposited under alkaline conditions. In situ oxygen uptake rates were measured at the tailings surface every third day, prior to sampling. In addition, cell counts of iron(II), sulfur, and thiosulfate oxidizing, lithotrophic bacteria and chemoorganotrophic microorganisms were determined quantitatively by the most-probable-number technique or by agar-plating. Results show consistent pyrite oxidation rates based on in situ oxygen uptake rates, and laboratory heat output measurements. Litho- and organotrophic bacteria were found in the tailings. Calorimetric measurements revealed that the present bacterial activity is responsible for approximately one third of the ongoing oxidation. Although leaching bacteria have previously been found in the Arctic, this study is the first to prove the significance of bacterial activity in the overall pollution resulting from tailings deposited in the Arctic.

Oxidative metabolism of inorganic sulfur compounds by bacteria.

The history of the elucidation of the microbiology and biochemistry of the oxidation of inorganic sulfur compounds in chemolithotrophic bacteria is briefly reviewed, and the contribution of Martinus Beijerinck to the study of sulfur-oxidizing bacteria highlighted. Recent developments in the biochemistry, enzymology and molecular biology of sulfur oxidation in obligately and facultatively lithotrophic bacteria are summarized, and the existence of at least two major pathways of thiosulfate (sulfur and sulfide) oxidation confirmed. These are identified as the 'Paracoccus sulfur oxidation' (or PSO) pathway and the 'S4intermediate' (or S4I) pathway respectively. The former occurs in organisms such as Paracoccus (Thiobacillus) versutus and P. denitrificans, and possibly in Thiobacillus novellus and Xanthobacter spp. The latter pathway is characteristic of the obligate chemolithotrophs (e.g. Thiobacillus tepidarius, T. neapolitanus, T. ferrooxidans, T. thiooxidans) and facultative species such as T. acidophilus and T. aquaesulis, all of which can produce or oxidize tetrathionate when grown on thiosulfate. The central problem, as yet incompletely resolved in all cases, is the enzymology of the conversion of sulfane-sulfur (as in the outer [S-] atom of thiosulfate [-S-SO3-]), or sulfur itself, to sulfate, and whether sulfite is involved as a free intermediate in this process in all, or only some, cases. The study of inorganic sulfur compound oxidation for energetic purposes in bacteria (i.e. chemolithotrophy and sulfur photolithotrophy) poses challenges for comparative biochemistry. It also provides evidence of convergent evolution among diverse bacterial groups to achieve the end of energy-yielding sulfur compound oxidation (to drive autotrophic growth on carbon dioxide) but using a variety of enzymological systems, which share some common features. Some new data are presented on the oxidation of 35S-thiosulfate, and on the effect of other anions (selenate, molybdate, tungstate, chromate, vanadate) on sulfur compound oxidation, including observations which relate to the roles of polythionates and elemental sulfur as intermediates.

La flore bactérienne des eaux thermales et minérales

Mineral and thermal waters are not sterile, but contain an indigenous microbial flora of a kind related to the physical and chemical characteristics of these biotopes.This microflora can be divided into two groups on a metabolic basis: first, lithotrophic bacteria which draw their energy from inorganic substances, and secondly organotrophic bacteria which use organic matter. The former play an important role in the cycle of elements such as sulphur and iron, and in the formulation of certain thermal compounds such as glairins, but have been little studied owing to the slowness of their growth on synthetic media. The second group, which can be demonstrated by simple and rapid methods of culture, consist essentially of gram-negative bacilli (Pseudomonas, Xanthomonas, Acinetobacter, etc.) and show high numerical stability with time. They have no health significance but any sudden rise in their number can indicate contamination of the resource.Better knowledge of these two types of bacterial flora could make it possible to select biological identity markers from the species characteristic of the resource and lead to a better understanding of their role in the operation of this natural ecosystem.

Growth of lithotrophic ammonia-oxidizing bacteria on hydroxylamine

Growth of lithotrophic ammonia-oxidizing bacteria on hydroxylamine

Biodeterioration of concrete by thiobacilli and nitrifying bacteria

The biological attack may contribute considerably to the deterioration of ceramic materials. Especially lithotrophic bacteria have been demonstrated to be of importance due to the excretion of sulfuric or nitric acid. The Biogenic Sulfuric Acid Corrosion and the Nitric Acid Corrosion of concrete were remodeled in simulation apparatus’. The biotest allowed to detect within many different types of materials the appropiate ones. Because the biotest includes the interactions of microorganisms and their environment, a part is the ceramic material as substratum, it cannot be replaced by chemical and/or physical testing.

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Abstract Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N2‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H2‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 103 most probable number (MPN) g‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 106 colony forming units (CFU) g‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N2‐fixing bac...

A Modified DAPI Fluorescence Staining Procedure Suitable for the Visualization of Lithotrophic Bacteria

Summary A DAPI fluorescence staining method, modified by a combination with low concentrations of SDS, is described which is suitable for the microscopic visualization of lithotrophic organisms growing on ores.