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More than two decades ago, Kenneth Nealson and Charles Myers published a seminal manuscript, describing an organism that can couple growth to the respiratory reduction of manganese oxide, an extracellular electron acceptor. This was the starting point of research aiming to elucidate mechanisms of extracellular respiration in a γ-proteobacterium named Shewanella oneidensis. This research is manifested in a nearly confusing multitude of publications that are sometimes even contradictory. It is the aim of this chapter to give a thorough overview of our knowledge about the biochemistry of metal respiration in S. oneidensis. This chapter starts off with a technological survey describing the molecular toolbox we have in our hands to genetically modify S. oneidensis. Thereafter, the path of electrons from the cytoplasmic membrane to the cell surface is followed, and thereby potential proteins for this electron transport and the transfer onto terminal metallic electron acceptors are brought to the reader’s attention. Moreover, the potential role of further proteins is analyzed that are not necessarily involved in the electron transport chain to ferric iron or manganese oxides per se but still seem to provide a selective advantage for the organism. Throughout the text it will become clear that the list of open questions concerning S. oneidensis physiology is still, even after decades of research and although it is the best studied dissimilatory metal reducer, extensive, and that there is room for more fascinating questions that can be addressed using the system S. oneidensis.

The longer we study the processes of microbial metal reduction the more we see the diversity within the processes. There are model organisms that are widely used to study the biochemistry of microbial metal respiration, but these strains are only the tip of the iceberg in terms of phylogenetic diversity. Dissimilatory metal reducers are highly abundant and widespread within the tree of life. Interestingly, the phylogenetic diversity seems to be mirrored by a biochemical diversity, which we are just beginning to assess. Diversity can also be seen in the terminal electron acceptors that can be used. Certainly, iron and manganese are the most influential environmental metallic electron acceptors and were therefore covered in the first chapter of this book. Nevertheless, other metals can serve as respiratory electron acceptors as well. These metals are mostly toxic and their reduction might not only be of respiratory purpose but also a detoxification process. Interestingly, in the past years, reduction of these alternative metallic electron acceptors became more and more an applied process for bioremediation, metal enrichment, and catalyst production. Therefore, this chapter deals with diversity and highlights phylogenetic diversity as well as the diversity within the usable metallic electron acceptors.

Iron–sulfur clusters are important biological cofactors that are used for electron transfer and also for reactivity. Though the iron atoms in these clusters are typically a mixture of ferrous iron(II) and ferric iron(III), there have been reports of biological iron–sulfur clusters in which all the iron atoms are reduced to the iron(II) oxidation state. These reports have inspired synthetic studies on all-ferrous iron–sulfur clusters. This chapter describes both the biological and synthetic work on all-iron(II) clusters, drawing comparisons and noting promising avenues for future research.

Neutrophilic iron-depositing microorganisms include various groups of bacteria, algae, and protozoa. The most striking feature of these microorganisms is their ability to precipitate ferric iron around their cells and colonies in many different forms. Growth of these microorganisms has various practical implications, for example, formation of iron ore in many parts of the world, aging of water wells, and clogging of drinking water pipes. Morphological description of many genera and species of iron-depositing bacteria by microscopy dates back to the nineteenth century, but only very few pure cultures of bacteria such as Leptothrix discophora and Gallionella ferruginea have been obtained in the last decades. Therefore, little has been known on the physiology or phylogeny of these bacteria.

In this paper we suggest that iron-seepages, a precursor form of bog iron ore, must have been among the earliest iron ores used in early bloomery furnaces in Ireland. This is because: of their bright orange colour; the dramatic red-staining of the associated water-red springs or meinn in Gaelic; their rapid regenerative nature which means that they would have been “harvested” on a cyclical basis rather than “mined”; and also because there is an absence of solid bog ore remains within the relict furnaces. Archaeological evidence for iron-seepage ore, consisting of fine powdery material, in early bloomery furnaces would be elusive on account of its clay-like pasty nature and the fact that it will easily merge into a background of soil and metallurgical waste. We assume that the original wet clay-like pasty mass would have been dried prior to charging in the furnace and purer than our modern sample; and also, possibly, but not necessarily, shaped into small lumps.

Natural microbial communities generally have an unknown structure and composition because of their still not yet cultivable members. Therefore, understanding the relationships among the bacterial members, prediction of their behaviour, and controlling their functions are difficult and often only partly successful endeavours to date. This study aims to test a new idea that allows to follow community dynamics on the basis of a simple concept. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S ribosomal RNA genes was used to describe a community profile that we define as composition of a community. Flow cytometry and analysis of DNA contents and forward scatter characteristics of the single cells were used to describe a community profile, which we define as structure of a community. Both approaches were brought together by a non-metric multidimensional scaling (n-MDS) for trend interpretation of changes in the complex community data sets. This was done on the basis of a graphical evaluation of the cytometric data, leading to the newly developed Dalmatian plot tool, which gave an unexpected insight into the dynamics of the unknown bacterial members of the investigated natural microbial community. The approach presented here was compared with other techniques described in the literature. The microbial community investigated in this study was obtained from a BTEX contaminated anoxic aquifer. The indigenous bacteria were allowed to colonise in situ microcosms consisting of activated carbon. These microcosms were amended with benzene and one of the electron acceptors nitrate, sulphate or ferric iron to stimulate microbial growth. The data obtained in this study indicated that the composition (via T-RFLP) and structure (via flow cytometry) of the natural bacterial community were influenced by the hydro-geochemical conditions in the test site, but also by the supplied electron acceptors, which led to distinct shifts in relative abundances of specific community members. It was concluded that engineered environments can be successfully monitored by single cell analytics in combination with established molecular tools and sophisticated statistical analyses, a combination that holds great promise for studying and monitoring natural microbial community behaviour.

Under iron limitation, most microorganisms synthesize siderophores which form soluble complexes with Fe+++ with very high formation constants. Thus iron is solubilized, and subsequently taken up by microbial transport systems which recognize the various Fe-siderophores.

One of the problems caused by strip mining is the generation of acidic lakes. Typically, the huge holes left from strip mining of soft coal are partly filled by mine tailings containing pyrite and other sulphide minerals. The remaining holes are flooded by groundwater forming so-called mine lakes. When in contact with oxygen-rich water the iron-sulphide species of the mine tailings are oxidized to sulphuric acid and ferric iron (Singer and Stumm 1970; Nordstrom et al. 1979). This results in an extreme acidification of the lakes (van Berk 1987; Obermann et al. 1992; Wisotzky 1994).

Transferrin is the major iron binding protein in vertebrate serum. It carries ferric iron from the intestine, reticuloendothelial system and liver parenchimal cells to all proliferating cells in the body.

Presently, chemical leaching of uranium, particularly from an acidic gangue, involves acidic ferric iron solutions. The 6-valent uranium is soluble at the acidic pH values involved, whereas solubilization of 4-valent uranium involved oxidation to the 6-valent species with ferric iron as the primary oxidant. Under most commercial vat leaching conditions, the pH is modestly below the level at which microbiological leaching can occur. In heap or “in situ” leaching, microbiological leaching is responsible for a substantial proportion (in mine drainage situations for all) of the uranium solubilized. The bacterium, Thiobacillus ferrooxidans, oxidizes the sulfides of most metals to the corresponding sulfates, thus generating acidic solutions. Where iron sulfides are involved the iron moiety is solubilized and concomitantly oxidized to the ferric form. The acidic ferric solutions, thus generated, solubilize both the 4- and 6-valent forms of uranium. The pH values over which this microbiological action can normally proceed are in the approximate range of 1.8 to 2.6; the upper limit being the less absolute. As the 4-valent uranium is oxidized to the 6-valent form, the iron which is reduced to the ferrous form is quickly reoxidized to the ferric state by Thiobacillus ferrooxidans, thus enabling leaching to continue. Microbiological oxidation of ferrous to ferric iron is in no way dependent on the original source of the ferrous iron. Thus microbiological oxidation can interact with chemical leaching processes, where pH and other conditions permit.

Uranium commonly occurs in the tetravalent form [U(IV)] in uranium-bearing rocks and the solubilization involves its oxidation to the hexavalent uranyl ion.

The accuracy of determination of the minor constituent of binary pairs of ions, by chromatography of organo-metallic complexes and colorimetric estimation of the separated pairs, is reported. The pair nickelferric iron, not separated by the technique previously used, may be separated using a less highly activated alumina. Appreciable errors occur in the determination of ferric iron and of nickel, and the pair coppernickel still remains unresolved.