Metals, minerals and microbes: geomicrobiology and bioremediation

Abstract

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. Microbes as geoactive agentsMicrobes interact with metals and minerals in natural and synthetic environments, altering their physical and chemical state, with metals and minerals also able to affect microbial growth, activity and survival. In addition, many minerals are biogenic in origin, and the formation of such biominerals is of global geological and industrial significance, as well as providing important structural components for many organisms, including important microbial groups such as diatoms, foraminifera and radiolaria (Ehrlich, 1996;Gadd & Raven, 2010). Geomicrobiology can simply be defined as the roles of microbes in geological processes (Banfield & Nealson, 1997;Banfield et al., 2005; Konhauser, 2007;Ehrlich & Newman, 2009). Metalminera...

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts

“…Fungi are significant agents of geochemical change in the environment and capable of numerous transformations of metals and minerals (Gadd 2007, 2010). They can therefore contribute to the structural and chemical alteration of rocks, and mineral-based substrates including those produced biogenically.…”

“…They can therefore contribute to the structural and chemical alteration of rocks, and mineral-based substrates including those produced biogenically. The study of the roles of fungi in geologically relevant processes, such as metal and mineral transformations, can be termed geomycology, an important part of the more general area of geomicrobiology (Gadd 2007, 2010). In the terrestrial environment, such processes are important in rock bioweathering, contributing to the formation and development of mineral soil, and global biogeochemical cycles for component elements, including their availability to living organisms (Sterflinger 2000; Burford et al 2003; Gadd 2007).…”

“…Fungal activities in rock and mineral transformations can therefore lead to increased mobility of such elements, and other minor crustal components, as well as the formation of secondary mineral products. Fungi can play a role in the dissolution of common minerals including carbonates, phosphates and silicates and less common compounds including oxides and oxalates (Gadd 2010; Gadd et al 2014; Bindschedler et al 2016). Lichens are a symbiosis of a fungus with either a cyanobacterium or a trebouxian green algae (see earlier) and actively digest rock surfaces.…”

“…Lichens can cause mechanical damage due to penetration by their anchoring structures, composed of fungal hyphae (Chen et al 2000). Biochemical weathering of rock and mineral substrates occurs through excretion of hydrogen ions, CO 2 , organic acids, siderophores and other metabolites, for example, resulting in pitting, etching or dissolution (Gadd 2010). Some organic metabolites affect dissolution by complexing with constituent metals, permitting removal of the mineral in a mobile form.…”

Cleanup of industrial effluents containing heavy metals: a new opportunity of valorising the biomass produced by brewing industry

“…Cu, Fe, Zn, Co, and Mn) are essential trace elements, at lower concentrations, necessary to the nor-mal growth and cell metabolism; however, these metals, be-come toxic above specific threshold concentrations. Other metals, such as Cd, Hg, and Pb are non-essential for biological functions and are highly toxic, even at low concentrations (Gadd 2010). Metal ions (essential and non-essential), unlike organic compounds, are not biodegradable and can be accu-mulated through the food chain, creating an environmental hazard and posing a serious risk to public health (Naja and Volesky 2010a;Colin et al 2012).…”