Joyce M. McBeth

Iron-oxidizing bacteria: an environmental and genomic perspective.

In the 1830s, iron bacteria were among the first groups of microbes to be recognized for carrying out a fundamental geological process, namely the oxidation of iron. Due to lingering questions about their metabolism, coupled with difficulties in culturing important community members, studies of Fe-oxidizing bacteria (FeOB) have lagged behind those of other important microbial lithotrophic metabolisms. Recently, research on lithotrophic, oxygen-dependent FeOB that grow at circumneutral pH has accelerated. This work is driven by several factors including the recognition by both microbiologists and geoscientists of the role FeOB play in the biogeochemistry of iron and other elements. The isolation of new strains of obligate FeOB allowed a better understanding of their physiology and phylogeny and the realization that FeOB are abundant at certain deep-sea hydrothermal vents. These ancient microorganisms offer new opportunities to learn about fundamental biological processes that can be of practical importance.

Neutrophilic Iron-Oxidizing “Zetaproteobacteria” and Mild Steel Corrosion in Nearshore Marine Environments

ABSTRACT Microbiologically influenced corrosion (MIC) of mild steel in seawater is an expensive and enduring problem. Little attention has been paid to the role of neutrophilic, lithotrophic, iron-oxidizing bacteria (FeOB) in MIC. The goal of this study was to determine if marine FeOB related to Mariprofundus are involved in this process. To examine this, field incubations and laboratory microcosm experiments were conducted. Mild steel samples incubated in nearshore environments were colonized by marine FeOB, as evidenced by the presence of helical iron-encrusted stalks diagnostic of the FeOB Mariprofundus ferrooxydans, a member of the candidate class “Zetaproteobacteria.” Furthermore, Mariprofundus-like cells were enriched from MIC biofilms. The presence of Zetaproteobacteria was confirmed using a Zetaproteobacteria-specific small-subunit (SSU) rRNA gene primer set to amplify sequences related to M. ferrooxydans from both enrichments and in situ samples of MIC biofilms. Temporal in situ incubation studies showed a qualitative increase in stalk distribution on mild steel, suggesting progressive colonization by stalk-forming FeOB. We also isolated a novel FeOB, designated Mariprofundus sp. strain GSB2, from an iron oxide mat in a salt marsh. Strain GSB2 enhanced uniform corrosion from mild steel in laboratory microcosm experiments conducted over 4 days. Iron concentrations (including precipitates) in the medium were used as a measure of corrosion. The corrosion in biotic samples (7.4 ± 0.1 mM) was significantly higher than that in abiotic controls (5.0 ± 0.1 mM). These results have important implications for the role of FeOB in corrosion of steel in nearshore and estuarine environments. In addition, this work shows that the global distribution of Zetaproteobacteria is far greater than previously thought.

Biodiversity and emerging biogeography of the neutrophilic iron-oxidizing Zetaproteobacteria

ABSTRACT Members of the neutrophilic iron-oxidizing candidate class Zetaproteobacteria have predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (>1,400-bp) and 48 partial-length Zetaproteobacteria small-subunit (SSU) rRNA gene sequences from five novel clone libraries, one novel Zetaproteobacteria isolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of the Proteobacteria and to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) on the basis of a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply rooted OTUs that potentially dominate communities of iron oxidizers originating in the deep subsurface were identified. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution of Zetaproteobacteria biodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that the Zetaproteobacteria have a strong biogeographic signal.

The Microbial Ferrous Wheel in a Neutral pH Groundwater Seep

Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II) at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II) just at its surface (∼5 cm depth), suggesting an internal Fe(II) source coupled to active Fe(III) reduction. Most probable number enumerations detected microaerophilic Fe(II)-oxidizing bacteria (FeOB) and dissimilatory Fe(III)-reducing bacteria (FeRB) at densities of 102 to 105 cells mL−1 in samples from both sites. In vitro Fe(III) reduction experiments revealed the potential for immediate reduction (no lag period) of native Fe(III) oxides. Conventional full-length 16S rRNA gene clone libraries were compared with high throughput barcode sequencing of the V1, V4, or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g., Gallionella, Sideroxydans, Aquabacterium). Sequences related to recognized FeRB (e.g., Rhodoferax, Aeromonas, Geobacter, Desulfovibrio) were also well-represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode libraries provided confirmation of key clone library results (e.g., the predominance of Betaproteobacteria) and an expanded view of lithotrophic microbial community composition.

Probing the Biogeochemical Behavior of Technetium Using a Novel Nuclear Imaging Approach

Dynamic gamma-camera imaging of radiotracer technetium ((99m)Tc) was used to assess the impact of biostimulation of metal-reducing bacteria on technetium mobility at 10(-12) mol L(-1) concentrations in sediments. Addition of the electron donor acetate was used to stimulate a redox profile in sediment columns, from oxic to Fe(III)-reducing conditions. When (99m)Tc was pumped through the columns, real-time gamma-camera imaging combined with geochemical analyses showed technetium was localized in regions containing biogenic Fe(II). In parallel experiments, electron microscopy with energy-dispersive X-ray (EDX) mapping confirmed sediment-bound Tc was associated with iron, while X-ray absorption spectroscopy (XAS) confirmed reduction of Tc(VII) to poorly soluble Tc(IV). Molecular analyses of microbial communities in these experiments supported a direct link between biogenic Fe(II) accumulation and Tc(VII) reductive precipitation, with Fe(III)-reducing bacteria more abundant in technetium immobilization zones. This offers a novel approach to assessing radionuclide mobility at ultratrace concentrations in real-time biogeochemical experiments, and confirms the effectiveness of biostimulation of Fe(III)-reducing bacteria in immobilizing technetium.

The transition from freshwater to marine iron-oxidizing bacterial lineages along a salinity gradient on the Sheepscot River, Maine, USA

Oxygen-dependent, neutrophilic iron-oxidizing bacteria (FeOB) are important drivers of iron transformations in marine and freshwater environments. Despite remarkable similarities in physiology and morphotype, known freshwater and marine FeOB are clustered in different classes of Proteobacteria; freshwater FeOB in the Betaproteobacteria and marine FeOB in the Zetaproteobacteria. To determine effects of salinity on these microbes, we examined the mineral biosignatures and molecular ecology of bacteria in FeOB mats collected along an estuarine salinity gradient. Light microscopy and scanning electron microscopy analyses showed the presence of iron oxide stalk and sheath structures in both freshwater and saline iron mats. Results of tagged pyrosequencing, quantitative PCR and fluorescent in situ hybridization, all based on the small subunit rRNA gene, confirmed Zetaproteobacteria were not present in freshwater mats, but were in saline mats at salinities down to 5‰. Among the Betaproteobacteria, Leptothrix spp. were only found in the freshwater mat. Gallionella spp. were limited to freshwater and low salinity mats (< 5‰). Sideroxydans sp. were salt tolerant; however, their relative abundance decreased with increasing salinity. These results suggest salinity is important in shaping the population biology of iron mat communities, and some coexistence between marine and freshwater populations occurs in brackish waters.

Redox interactions of technetium with iron-bearing minerals

Abstract Iron minerals influence the environmental redox behaviour and mobility of metals including the long-lived radionuclide technetium. Technetium is highly mobile in its oxidized form pertechnetate (Tc(VII)O4-), however, when it is reduced to Tc(IV) it immobilizes readily via precipitation or sorption. In low concentration tracer experiments, and in higher concentration XAS experiments, pertechnetate was added to samples of biogenic and abiotically synthesized Fe(II)-bearing minerals (bio-magnetite, bio-vivianite, bio-siderite and an abiotically precipitated Fe(II) gel). Each mineral scavenged different quantities of Tc(VII) from solution with essentially complete removal in Fe(II)-gel and bio-magnetite systems and with 84±4% removal onto bio-siderite and 68±5% removal onto bio-vivianite over 45 days. In select, higher concentration, Tc XAS experiments, XANES spectra showed reductive precipitation to Tc(IV) in all samples. Furthermore, EXAFS spectra for bio-siderite, bio-vivianite and Fe(II)-gel showed that Tc(IV) was present as short range ordered hydrous Tc(IV)O2-like phases in the minerals and for some systems suggested possible incorporation in an octahedral coordination environment. Low concentration reoxidation experiments with air-, and in the case of the Fe(II) gel, nitrate-oxidation of the Tc(IV)-labelled samples resulted in only partial remobilization of Tc. Upon exposure to air, the Tc bound to the Fe-minerals was resistant to oxidative remobilization with a maximum of ∼15% Tc remobilized in the bio-vivianite system after 45 days of air exposure. Nitrate mediated oxidation of Fe(II)-gel inoculated with a stable consortium of nitrate-reducing, Fe(II)-oxidizing bacteria showed only 3.8±0.4% remobilization of reduced Tc(IV), again highlighting the recalcitrance of Tc(IV) to oxidative remobilization in Fe-bearing systems. The resultant XANES spectra of the reoxidized minerals showed Tc(IV)-like spectra in the reoxidized Fe-phases. Overall, this study highlights the role that Fe-bearing biogenic mineral phases have in controlling reductive scavenging of Tc(VII) to hydrous TcO2-like phases onto a range of Fe(II)-bearing minerals. In addition, it suggests that on reoxidation of these phases, Fe-bound Tc(IV) may be octahedrally coordinated and is largely recalcitrant to reoxidation over medium-term timescales. This has implications when considering remediation approaches and in predictions of the long-term fate of Tc in the nuclear legacy.

Uranium redox cycling in sediment and biomineral systems

Under anaerobic conditions, uranium solubility is significantly controlled by the microbially mediated reduction of relatively soluble U(VI) to poorly soluble U(IV). However, the reaction mechanism(s) for bioreduction are complex with prior sorption of U(VI) to sediments significant in many systems, and both enzymatic and abiotic U(VI) reduction pathways potentially possible. Here, we describe results from sediment microcosm and Fe(II)-bearing biomineral experiments designed to assess the relative importance of enzymatic vs. abiotic U(VI) reduction mechanisms and the long-term fate of U(IV). In oxic sediments representative of the UK Sellafield reprocessing site, U(VI) was rapidly and significantly sorbed to surfaces and during microbially-mediated bioreduction, XAS analysis showed that sorbed U(VI) was reduced to U(IV) commensurate with Fe(III)-reduction. Additional control experiments with Fe(III)-reducing sediments that were sterilized after bioreduction and then exposed to U(VI), indicated that U(VI) reduction was inhibited, implying that enzymatic as opposed to abiotic mechanisms dominated in these systems. Further experiments with model Fe(II)-bearing biomineral phases (magnetite and vivianite) showed that significant U(VI) reduction occurred in co-precipitation systems, where U(VI) was spiked into the biomineral precursor phases prior to inoculation with Geobacter sulfurreducens. In contrast, when U(VI) was exposed to pre-formed, washed biominerals, XAS analysis indicated that U(VI) was recalcitrant to reduction. Reoxidation experiments examined the long-term fate of U(IV). In sediments, air exposure resulted in Fe(II) oxidation and significant U(IV) oxidative remobilization. By contrast, only partial oxidation of U(IV) and no remobilization to solution occurred with nitrate mediated bio-oxidation of sediments. Magnetite was resistant to biooxidation with nitrate. On exposure to air, magnetite changed from black to brown in colour, yet there was limited mobilization of uranium to solution and XAS confirmed that U(IV) remained dominant in the oxidized mineral phase. Overall these results highlight the complexity of uranium biogeochemistry and highlight the importance of mechanistic insights into these reactions if optimal management of the global nuclear legacy is to occur.

In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria

Microbiologically influenced corrosion (MIC) is a complex biogeochemical process involving interactions between microbes, metals, minerals, and their environment. We hypothesized that sediment-derived iron-oxidizing bacteria (FeOB) would colonize and become numerically abundant on steel surfaces incubated in coastal marine environments. To test this, steel coupons were incubated on sediments over 40 days, and samples were taken at regular intervals to examine microbial community succession. The experiments were conducted at two locations: (1) a brackish salt marsh stream and (2) a coastal marine bay. We analyzed DNA extracted from the MIC biofilms for bacterial diversity using high-throughput amplicon sequencing of the SSU rRNA gene, and two coupons from the coastal site were single cell sorted and screened for the SSU rRNA gene. We quantified communities of Zetaproteobacteria, sulfate-reducing bacteria (SRB), and total bacteria and archaea using qPCR analyses. Zetaproteobacteria and SRB were identified in the sequencing data and qPCR analyses for samples collected throughout the incubations and were also present in adjacent sediments. At the brackish site, the diversity of Zetaproteobacteria was lower on the steel compared to sediments, consistent with the expected enrichment of FeOB on steel. Their numbers increased rapidly over the first 10 days. At the marine site, Zetaproteobacteria and other known FeOB were not detected in sediments; however, the numbers of Zetaproteobacteria increased dramatically within 10 days on the steel surface, although their diversity was nearly clonal. Iron oxyhydroxide stalk biosignatures were observed on the steel and in earlier enrichment culture studies; this is evidence that the Zetaproteobacteria identified in the qPCR, pyrosequencing, and single cell data were likely FeOB. In the brackish environment, members of freshwater FeOB were also present, but were absent in the fully marine site. This work indicates there is a successional pattern in the colonization of steel surfaces with FeOB being early colonizers; over time the MIC community matures to include other members that may help accelerate corrosion. This work also shows there is a reservoir for Zetaproteobacteria in coastal sediment habitats, where they may influence the coastal iron cycle, and can rapidly colonize steel surfaces or other sources of Fe(II) when available.

Iron cycling at corroding carbon steel surfaces

Surfaces of carbon steel (CS) exposed to mixed cultures of iron-oxidizing bacteria (FeOB) and dissimilatory iron-reducing bacteria (FeRB) in seawater media under aerobic conditions were rougher than surfaces of CS exposed to pure cultures of either type of microorganism. The roughened surface, demonstrated by profilometry, is an indication of loss of metal from the surface. In the presence of CS, aerobically grown FeOB produced tight, twisted helical stalks encrusted with iron oxides. When CS was exposed anaerobically in the presence of FeRB, some surface oxides were removed. However, when the same FeOB and FeRB were grown together in an aerobic medium, FeOB stalks were less encrusted with iron oxides and appeared less tightly coiled. These observations suggest that iron oxides on the stalks were reduced and solubilized by the FeRB. Roughened surfaces of CS and denuded stalks were replicated with culture combinations of different species of FeOB and FeRB under three experimental conditions. Measurements of electrochemical polarization resistance established different rates of corrosion of CS in aerobic and anaerobic media, but could not differentiate rate differences between sterile controls and inoculated exposures for a given bulk concentration of dissolved oxygen. Similarly, total iron in the electrolyte could not be used to differentiate treatments. The experiments demonstrate the potential for iron cycling (oxidation and reduction) on corroding CS in aerobic seawater media.