Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi

Abstract

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and generally relies on microbe-mineral interactions that transform various iron oxide minerals. In this study, the physiology of dissimilatory iron and nitrate reduction was examined in the hyperthermophilic crenarchaeon Pyrodictium delaneyi Su06T. Iron barrier experiments showed that P. delaneyi required direct contact with the Fe(III) oxide mineral ferrihydrite for reduction. The separate addition of an exogenous electron shuttle (anthraquinone-2,6-disulfonate), a metal chelator (nitrilotriacetic acid), and 75% spent cell-free supernatant did not stimulate growth with or without the barrier. Protein electrophoresis showed that the c-type cytochrome and general protein compositions of P. delaneyi changed when grown on ferrihydrite relative to nitrate. Differential proteomic analyses using tandem mass tagged protein fragments and mass spectrometry detected 660 proteins and differential production of 127 proteins. Among these, two putative membrane-bound molybdopterin-dependent oxidoreductase complexes increased in relative abundance 60- to 3,000-fold and 50-100-fold in cells grown on iron oxide. A putative 8-heme c-type cytochrome was 60-fold more abundant in iron grown cells and was unique to the Pyrodictiaceae. There was also a >14,700-fold increase in a membrane transport protein in iron grown cells. There were no changes in the abundances of flagellin proteins nor a putative nitrate reductase, but a membrane nitric oxide reductase was more abundant on nitrate. These data help to elucidate the mechanisms by which hyperthermophilic crenarchaea generate energy and transfer electrons across the membrane to iron oxide minerals. IMPORTANCE Understanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a membrane-bound molybdopterin respiratory complex sets iron reduction in this organism apart from previously described iron reduction processes. A model is presented where obligatory H2 oxidation on the membrane coupled with electron transport and either Fe(III) oxide or nitrate reduction leads to the generation of a proton motive force and energy generation by oxidative phosphorylation. However, P. delaneyi cannot fix CO2 and relies on organic compounds from its environment for biosynthesis.

The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales

“…The second cluster (MCL4079376-90) encodes homologs of the same quinol oxidizing multiheme and the CFE_2239 multiheme, as well as a molybdopterin oxidoreductase and a weak homolog of SmhB cytochrome, involved in soluble ferric citrate reduction in C. ferrireducens ( Gavrilov et al, 2021 ). Simultaneous involvement of membrane-bound multiheme cytochrome c and molybdopterin enzyme complexes in Fe(III) oxide reduction has been recently proposed for the archaeon Pyrodictium delaneyi ( Kashyap and Holden, 2021 ). Probably, peculiar organization of the cluster MCL4079376-90 in the strain Es71-Z0120 T is the main feature determining the Fe(III) reducing ability in contrast to its non-Fe(III) reducing counterpart.…”

Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring

“…It is important to note that P. yellowstonensis WP30, which also encodes the DC/4HB pathway, could not be cultivated autotrophically when grown anaerobically on elemental sulfur or As(V) ( 18 ). However, many archaea, including sulfur- and iron-reducing archaea ( 48 , 49 ), are known to harbor mixotrophic carbon and energy metabolisms, and mixotrophic metabolism was not specifically examined in the study of P. yellowstonensis WP30.…”

The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation

“…Thus, P. islandicum must employ c -Cyt-independent mechanisms for direct reduction of Fe(III) (oxyhydr)oxides ( Feinberg et al, 2008 ). Indeed, molybdopterin oxidoreductases of Pyrodictium delaneyi are suggested to transfer electrons directly to Fe(III) (oxyhydr)oxides ( Kashyap and Holden, 2021 ).…”