Geomycology: Fungi as Agents of Biogeochemical Change

Geomycology is the study of the roles of fungi in geological processes. The biogeochemical importance of fungi is significant in several areas, including nutrient and element cycling, rock, mineral and metal transformations, bioweathering and mycogenic biomineral formation. Such processes can occur in aquatic and terrestrial habitats, but it is the terrestrial environment where fungi probably have the greatest geochemical influence. Of special significance are the mutualistic relationships with phototrophic organisms: lichens (algae, cyanobacteria) and mycorrhizas (plants). Central to many geomycological processes are transformations of metals and minerals, and fungi possess many properties that effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Some fungal transformations have potential applications in environmental biotechnology, e.g. metal and radionuclide leaching, recovery, detoxification and bioremediation, and in the production or deposition of biominerals or metallic elements with catalytic or other properties. Metal and mineral transformations may also result in adverse effects when these processes result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment.

Geomycology can be simply defined as 'the scientific study of the roles of fungi in processes of fundamental importance to geology' and the biogeochemical importance of fungi is significant in several key areas. These include nutrient and element cycling, rock and mineral transformations, bioweathering, mycogenic biomineral formation and interactions of fungi with clay minerals and metals. Such processes can occur in aquatic and terrestrial habitats, but it is in the terrestrial environment where fungi probably have the greatest geochemical influence. Of special significance are the mutualistic relationships with phototrophic organisms, lichens (algae, cyanobacteria) and mycorrhizas (plants). Central to many geomycological processes are transformations of metals and minerals, and fungi possess a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Some fungal transformations have beneficial applications in environmental biotechnology, e.g. in metal and radionuclide leaching, recovery, detoxification and bioremediation, and in the production or deposition of biominerals or metallic elements with catalytic or other properties. Metal and mineral transformations may also result in adverse effects when these processes result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment. The ubiquity and importance of fungi in biosphere processes underlines the importance of geomycology as an interdisciplinary subject area within microbiology and mycology.

Oxalate production by fungi: significance in geomycology, biodeterioration and bioremediation

Eukaryotic microbes participate in many biogeochemical cycles, although quantifying their role is not easy, and the discussion below comes generally to only qualitative conclusions. Eukaryotes lack a number of the biogeochemically important functions that are carried out only by archaea (e.g., methanogenesis), bacteria (the anammox chemolithotrophic denitrification reaction), or archaea and bacteria (e.g., chemolithotrophy, diazotrophy, and dissimilatory reduction of sulfate). Microbial eukaryotes have one ancestral attribute, phagotrophy, which adds a novel link to food webs and thus modifies biogeochemical cycles, and have endosymbioses as well as ectosymbioses which can recruit metabolism from archaeans (methanogenesis) and bacteria (chemolithotrophic sulfide oxidation, diazotrophy). The ability of eukaryotes to carry out oxidative phosphorylation and the related respiratory carbon metabolism, and photosynthesis, as genetically integrated processes is an outcome of bacterial symbioses. The biogeochemical importance of fungi is significant in several key areas. These include organic and inorganic transformations, nutrient and element cycling, rock and mineral transformations, bioweathering, mycogenic mineral formation, fungal-clay interactions, and metal-fungal interactions. Although such transformations can occur in both aquatic and terrestrial habitats, it is in the terrestrial environment where fungi probably have the greatest influence especially when considering soil, rock and mineral surfaces, and the plant root-soil interface. Of special significance are the mutualistic symbioses, lichens and mycorrhizas. Geochemical transformations that take place can influence plant productivity and the mobility and speciation of toxic elements, and are therefore of considerable socioeconomic relevance. Some fungal transformations have beneficial applications in environmental biotechnology, e.g., in metal and radionuclide leaching, recovery and detoxification, and xenobiotic and organic pollutant degradation. They may also result in adverse effects when these processes are associated with the degradation of foodstuffs, natural products and building materials, including wood, stone and concrete.

Microbes play key geoactive roles in the biosphere particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and “higher organisms”, can contribute actively to geological phenomena, and central to many such geomicrobial processes are metal and mineral transformations. Microbial roles in mineral transformations and metal cycling are especially important in the Earth’s Critical Zone (CZ) and microbes possess a variety of properties that can effect changes in metal speciation, toxicity and mobility, mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in organic matter, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences for human society. Bioremediation refers to the application of biological systems to the clean-up of organic and inorganic pollution with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for structural, technological, environmental and antimicrobial purposes. In contrast, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials, e.g. concrete, acid mine drainage and associated metal pollution, biocorrosion of metals, alloys, and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. In view of the ubiquity and importance of microbes in such global processes, it can be proposed that an additional definition of the CZ could be “that portion of the terrestrial environment characterized by a significant microbial influence on metal and mineral transformations, organic matter decomposition, and the cycling of other elements”.

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

Geomicrobiology addresses the roles of microorganisms in geological and geochemical processes, and geomycology is a part of this topic focusing on the fungi. Geoactive roles of fungi include organic and inorganic transformations important in nutrient and element cycling, rock and mineral bioweathering, mycogenic biomineral formation, and metal-fungal interactions. Lichens and mycorrhizas are significant geoactive agents. Organic matter decomposition is important for cycling of major biomass-associated elements, e.g., C, H, N, O, P, and S, as well as all other elements found in lower concentrations. Transformations of metals and minerals are central to geomicrobiology, and fungi affect changes in metal speciation, as well as mediate mineral formation or dissolution. Such mechanisms are components of biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks, and minerals, e.g., S, P, and metalloids. Fungi may have the greatest geochemical influence within the terrestrial environment. However, they are also important in the aquatic environment and are significant components of the deep subsurface, extreme environments, and habitats polluted by xenobiotics, metals, and radionuclides. Applications of geomycology include metal and radionuclide bioleaching, biorecovery, detoxification, bioremediation, and the production of biominerals or metal(loid) elements with catalytic or other properties. Adverse effects include biodeterioration of natural and synthetic materials, rock and mineral-based building materials (e.g., concrete), cultural heritage, metals, alloys, and related substances and adverse effects on radionuclide mobility and containment. The ubiquity and importance of fungi in the biosphere underline the importance of geomycology as a conceptual framework encompassing the environmental activities of fungi.

Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation

Metals and Metalloids, Transformation by Microorganisms

Microbes play key geoactive roles in the biosphere in element and mineral biotransformations. Central to many geomicrobial processes are transformations of metals and minerals. Apart from being important in natural biosphere processes, metal and mineral transformations have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the cleanup of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization, or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline, or colloidal forms. Several metal and mineral transformations by microbes result in spoilage and destruction of natural and synthetic materials, rock and mineral‐based building materials, for example, concrete, acid mine drainage and associated metal pollution, biocorrosion of metals, alloys, and related substances, and adverse effects on radionuclide speciation, mobility, and containment.

Mycotransformation of organic and inorganic substrates

Fungi and Their Role in the Biosphere

Fungi are capable of the degradation, utilisation and/or transformation of a wide variety of organic and inorganic substances, including xenobiotics, metals, radionuclides, and minerals. Fungal populations are therefore intimately involved in element cycling at local and global scales, and such processes have major implications for living organisms, notably plant productivity and human health. It also follows that impairment of fungal activity could have serious consequences for ecosystem function in view of their importance in terrestrial habitats and as plant symbionts. Their activities are part of natural biogeochemical cycles for major elements such as C, N, O, P and S but also metals and radionuclides, as well as having application in the natural attenuation or bioremediation of polluted sites. Despite the toxicity of organic and inorganic pollutants, fungi are ubiquitous inhabitants of polluted locations and exhibit a variety of mechanisms underpinning tolerance and survival. Some fungal transformations of pollutants have applications in environmental biotechnology, e.g. metal bioleaching, biorecovery and detoxification and xenobiotic and organic pollutant degradation and bioremediation. This chapter outlines some important interactions of fungi with organic and inorganic pollutants and highlights the interdisciplinary approach that is necessary to further understand the important roles that fungi play in pollutant transformations, the chemical and biological mechanisms that are involved, and their environmental and applied significance.

Mineral formation during simulated leaks of Hanford waste tanks

Fungi and Their Role in the Biosphere