INTRODUCTION TO GEOMICROBIOLOGY

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The field of geomicrobiology concerns the role of microbe and microbial processes in geological and geochemical processes. The field is especially important when dealing with microorganisms in aquifers and public drinking water supplies. Geomicrobiology is the study of the interactions between microbes and minerals. It concerns itself with how microbes eat rocks. These rock-eating microbes are known as extremophiles; and they can generally be known as geomicrobes. Extremophiles are microorganisms that live in areas considered too hostile for most. An example of an extremophile is the anaerobic sulfate reducing bacteria, which are known to live in hyper-saline lagoons. These organisms live in areas with high salt concentrations. It is believed these bacteria may be responsible for the formation of dolmitea. A good example of a geomicrobe is Pseudomonas putidia. Geomicrobiology is a combination of geology and microbiology; and it studies the impact of microbes on rocks and other solid parts of the environment.  Geomicrobiological processes are relevant in many natural environments including aquifers, geological and geochemical processes, extreme environments (acidic, extreme temperatures and saline conditions) and metal ion reduction or extraction.

Microorganisms cause mineral precipitation and dissolution and control the distribution of elements in diverse environments at and below the surface of the Earth. Conversely, mineralogical and geochemical factors exert important controls on microbial evolution and the structure of microbial communities. Minerals have been known and honored since humans realized their essential contributions to the “terra firma” and stone tools thrust our species on the path of cultural evolution. Microbes are the oldest living creatures, probably inhabiting at least a few salubrious environments on the earth as early as 3.8 billion years ago. At this moment in history we are only beginning to appreciate the intimate juxtaposition and interdependence of minerals and microbes. We have been nudged into this position by the realization that our earth is finite, and the recognition of many global environmental problems that minerals and microbes contribute to, both positively and negatively. In addition, our globe may not be the only site in the solar system where ‘life’ arose, or may persist. What all of these concerns enunciate is that we as scientists only dimly comprehend our own dynamic “terrestrial halls.”

Over 3600 mineral species have been defined and their relationships to each other and the environments in which they form have been documented. This vast data base, collected over the past several hundred years and constantly added to and upgraded, is a monument to the research efforts of many geoscientists focused on the inorganic realm. Much of this data has come from investigators intrigued by the novelty, beauty, and versatility of minerals, direct expressions of the chemistry and physics of geologic processes. We are now adding a new dimension to questions of mineral formation, dissolution, and distribution: what were, are, and will be the contributions of microbes to these basic components of the environment. Microbes have also been known for hundreds of years. However, their small size (0.5 to 5 µm in diameter) and the difficulties associated with identifying a species unless it was grown in the laboratory (cultured), precluded thorough analysis. The advent of molecular biology has only recently made it possible to evaluate microbial evolutionary relatedness (phylogeny) and physiological diversity. These techniques are now being applied to study of microbial populations in natural environments. It is becoming very clear that the surface of Earth is populated by far more species of microbes than there are types of minerals.

We are now exploring every portion of the globe and finding the relationships under the rubric “geomicrobiology.” The ocean deeps are characterized by a diversity of microorganisms, including those associated with manganese nodules. The profusion and concentration of minerals created at ocean ridges and vents matches the variety of microorganisms, large animals, and plants there. The snowy tops of mountain ranges and glaciers of Antarctica harbor not just ice but whole bacterial communities whose cellular types and activities need elucidation. The equatorial jungles and the deserts, with their enormous diversity of ecological niches, further challenge us. The diversity of geographic, geologic, and biologic environments, including some contributed by humans (e.g. mines, air-conditioning equipment), can now also be explored in detail. Modern studies use protocols developed to preserve or measure in situ chemical and physical characteristics. Electron microscopes allow direct characterization of mineral and biological morphology and internal structures. Spectroscopic techniques permit complimentary chemical analysis, including determination of oxidation states, with very high spatial resolution. Other studies quantitatively measure isotopic abundances.

These data serve to distinguish biologically mediated or biologically controlled formation of the mineral from an abiotic process and mechanism. Each ecological niche requires accurate characterization of the mineralogic and biologic entities in order for us to begin to understand the range of dynamic relationships. We can pose many questions. Is the mineral only a substrate, or is its occurrence and stability impacted by microbiologic activity and metabolic requirements? Which minerals are of microbiological rather than inorganic origin and what are the mechanisms by which organisms dictate the morphology and structure of the solid phase formed? How do organic metabolic products bind metals and change their form and distribution, with implications for metal toxicity and geochemical cycles? How do inorganic reactions such as mineral dissolution and precipitation impact microbial populations through control of their physical and chemical environments?

PROCESSES IN WHICH GEOMICROBIOLOGY CAN BE APPLIED

Some of the most important processes in which geomicrobiology can be applied include: 1- Weathering 2- Precipitation of carbonates and phosphates 3- Ocean crust support 4- Nuclear waste disposal 5- Hot springs

Weathering

Weathering is defined as the breaking down or dissolving of rocks and minerals on Earths surface. Water, ice, acids, salt, plants, animals, and changes in temperature are all agents of weathering. Once the rock has been broken down, a process called erosion transports the bits of rock and minerals away. Weathering plays an important role on Earth ecosystems and is important for the release of nutrients into the biosphere as a result of rock dissolution or the regulation of long-term climate by the consumption of atmospheric carbon dioxide from silicate alterations. Weathering has been considered a strictly physical and chemical process. Nonetheless, many weathering processes can be affected by the presence of microbial communities. All types of rocks are susceptible to microbial weathering, including siliceous and calcareous rocks. In general microbial weathering is due to the formation of organic acids or the production of metal-chelating siderophores on the surface of rock or minerals. Siderophores are low-molecular weight iron-chelating compounds synthesized and exported by most microorganisms including fungi and bacteria for the uptake of iron in their environment. The two main structural classes of siderophores are catecholamides and hydroxamates. Other processes include oxidative or reductive conditions of metals on rocks or minerals.

Precipitation of carbonates and phosphates

The influence of Bacteria in mineral precipitation has been described in different natural habitats including aquatic environments and geological systems. Carbonate precipitation is controlled by bacteria processes and one of the mechanisms proposed is the production of ammonium by metabolizing nitrogen base organic compounds which increases environment pH.

Ocean crust support

Microbiological studies on sediment cores collected by the Deep Sea Drilling Program (DSDP) and the Ocean Drilling Program (ODP) have demonstrated the presence of microbial communities in deeply buried marine sediments. Prokaryotes in the marine sub-seafloor biosphere have been estimated to comprise one-tenth to one-third of the world’s living biomass and therefore probably play an important role in global biogeochemical processes. Microbial populations in these regions vary considerably as a result of sediment type and age, organic matter availability, temperature and sedimentation rate. An example of the processes involved in this type of ecosystems was proposed for the Juan de Fuca Ridge in the northeast pacific and can be found below

Nuclear waste disposal

Fungi can be very radiation-resistant and can survive and colonize concrete barriers under severe radioactive contamination. After ten years of the catastrophe of Chernobyl in 1986 extensive fungal growth was observed on the walls and other building structures constructed in the inner part of the “Shelter” built over the fourth Unit of the Chernobyl nuclear power plant. Safe long-term storage of both existing and future nuclear wastes is of vital importance in protecting the environment, therefore the study of these fungi has been key for future construction of nuclear waste repositories. The deterioration of concrete by fungi is performed by common mechanisms used by fungi for rock and mineral weathering. Some of the microorganisms isolated from these extreme environments include modified strains from the genera Alternaria, Cladosporium, and Aureobasidium

Microbial Energetics

Microbial energetic is defined as the mechanisms by which bacteria and other microbial cells derive the energy they require for growth from their environment. Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon, nitrogen, phosphorus) it needs to live and reproduce. Microbial energetic helps microbiologists to predict the growth yields of microbes. Bacteria can synthesize adenosine triphosphate (ATP) by a variety of routes that includes fermentation, oxidative phosphorylation, substrate level phosphorylation and possibly by the excretion of metabolic end products from their systems. An important part of microbial metabolism is microbial energenetics. Microbial energenetics are driven by Gibbs free-energy yield derived from ATP. ATP is heterotrophically generated by fermentation or respiration. The latter requires terminal electron acceptors (e.g. molecular oxygen, nitrate, sulphate, ferric iron, carbon dioxide, or molecular hydrogen), and produces greater amounts of ATP per unit substrate. Fermentation is less feasible in the presence of either highly oxidized or highly reduced substrate, and may rise toxic products (simple organic acids) that can eventually impede the process of the microbial growth. The energy in soil is preserved in both organic and inorganic components enabling the microbial communities to sustain catabolic and anabolic processes.

Metabolism isdefined as the subtotal of chemical reactions occurring in a living cell. These chemical reactions areenzyme-catalyzed i.e. they are spurred or controlled by the activities of enzymes. Enzymes are protein catalysts that speed up the rate of reaction in a living system. The different types of metabolism via which microbes synthesis or utilize molecules in their environment are (1) Anabolism (anabolic process) and (2) Catabolism (catabolic process). Anabolic process (anabolism) is defined as the metabolic process in which complex molecules from simpler molecules with the input of energy. Anabolism is an energy requiring process i.e. it uses energy to build up complex molecules. The synthesis of protein (a complex molecule) from simpler molecules such as amino acids is an example of an anabolic process. Catabolic process (catabolism) is defined as the metabolic process in which complex molecules are broken down to simpler molecules with the release of energy. The energy released by the cell during catabolism is used by the organism to do work.     

EXAMPLES OF GEOMICROBES AS RELATED TO THE ELEMENTS THEY METABOLIZE

Sulfur

Sulfate-reducing bacteria (SRB) comprise of several groups of bacteria that use sulfate as an oxidizing agent, reducing it to sulfide. Most sulfate-reducing bacteria can also use other oxidized sulfur compounds such as sulfite and thiosulfate, or elemental sulfur. This type of metabolism is called dissimilatory, since sulfur is not incorporated – assimilated – into any organic compounds. Sulfate-reducing bacteria have been considered as a possible way to deal with acid mine waters that are produced by other bacteria. Acidithiobacillus is a genus of Proteobacteria. The members of this genus used to belong to Thiobacillus, before they were reclassified in the year 2000. Members of this genus can be fined in pyrite deposits, metabolizing iron and sulfur and producing sulfuric acid.

Iron

Acidithiobacillus thiooxidans consumes sulfur and produces sulfuric acid. This bacterium in conjunction with others of the same genus is currently used in a mining technique called bioleaching whereby metals are extracted from their ores through oxidation. The bacteria are used as catalysts.

Manganese

Bacillus species and Pseudomonas putida are common soil and freshwater Mn(II)-oxidizing bacterium. Mn(II)-oxidizing bacteria are a diverse group found in almost all environments. These bacteria are up to 5 orders of magnitude faster than abiotic reactions in the production of Mn oxides which have an amorphous structure with a high surface area. Mn(II) oxides are the only known oxidants of Cr(III) in the environment. The mechanism of Mn(II) oxidation by these bacteria is not clear, although recent outcomes from studies with Bacillus sp. strain SG-1 have shown that a Mn(III) is an intermediate in the final oxidation of Mn(II) through enzymatic activity.

Uranium-Nitrate relationship

Contamination of aquifers by Uranium produced from nuclear weapons and fuel is becoming a real problem in different parts of the world. Aquifers are underground layers of rock that are saturated with water that can be brought to the surface through natural springs or by pumping. These aquifers are generally oxidized, therefore uranium predominantly exists as U(VI) usually coupled with carbonate making the compound quite soluble. Uranium reduction occurs under anaerobic conditions with Fe(III) and/or sulfate reduction. The biogeochemical processes that occur after uranium reduction are poorly understood. Recent research has shown that the addition of nitrate (a common co-contaminant with uranium) to U(IV)-containing sediments leads to the oxidation and remobilization of U(IV). Microorganisms responsible in this process are believed to be associated with nitrate dependent Fe(II)-oxidizing microorganisms

Phosphorus

Phosphorus is an important nutrient for all living organisms. Most Phosphorus found in living systems is in the form of inorganic phosphate and its esters. There are a number of studies showing biochemical reactions of P compounds that do not involve the formation of phosphate esters and these reactions involve compounds in which the P is at a lower valence state. On earth virtually all known phosphorus exists in the +5 oxidation state. Nonetheless, there are also two additional known forms phosphonates (+3) and phosphinates (+1). Studies have demonstrated the reduction of phosphate in anaerobic soil and during corrosion of metals under anaerobic conditions. A number of bacteria have been shown to be capable of oxidizing reduced P compounds when this is the sole source of P. Inorganic phosphite (+3) was oxidized to phosphate by numerous laboratory strains of microorganisms, including prokaryotes such as Escherichia coli, Agrobacterium tumefaciens, and several species of Pseudomonas and Rhizobium, as well as one eukaryote, Saccharomyces cerevisiae. Hypophosphite (+1) can also be oxidized to phosphate by Pseudomonas fluorescens, Bacillus caldolyticus and Pseudomonas stutzeri WM88. Apatite is the primary inorganic source of phosphorus in the biosphere. Soil fungi are known to increase plant-available phosphorus by promoting dissolution of various phosphate minerals. Some of the fungi involved are Zygomycetes in the order of Mucorales and Ascomycetes.

The Epsilon-proteobacteria have recently been recognized as globally ubiquitous in marine and terrestrial ecosystems. They play a major role in biogeochemical and geological processes and have been isolated from sulfur rich terrestrial and marine environments, some of which are considered extreme habitats. Most representatives are only known through the 16S rRNA gene sequence despite current effort to develop culture techniques. Hydrogenophilaceae also belongs to the Proteobacteria, and it is believed to be made of two genera. They are thermophilic bacterium growing in temperatures close to 50 °C. They obtain their energy from hydrogen oxidation. Example: Thiobacillus genus; includes only species from beta proteobacteria. This bacterium is used as a pest control in potato fields to control scabs.

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