Karrie A. Weber

Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction

Iron (Fe) has long been a recognized physiological requirement for life, yet for many microorganisms that persist in water, soils and sediments, its role extends well beyond that of a nutritional necessity. Fe(II) can function as an electron source for iron-oxidizing microorganisms under both oxic and anoxic conditions and Fe(III) can function as a terminal electron acceptor under anoxic conditions for iron-reducing microorganisms. Given that iron is the fourth most abundant element in the Earths crust, iron redox reactions have the potential to support substantial microbial populations in soil and sedimentary environments. As such, biological iron apportionment has been described as one of the most ancient forms of microbial metabolism on Earth, and as a conceivable extraterrestrial metabolism on other iron-mineral-rich planets such as Mars. Furthermore, the metabolic versatility of the microorganisms involved in these reactions has resulted in the development of biotechnological applications to remediate contaminated environments and harvest energy.

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 °C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37 mW m−2 with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray and clone library analysis with small subunit ribosomal RNA (16S rRNA) and ribosomal RNA gene (16S rDNA). The results illustrated the dominance (80% of clone library sequences) of the Firmicutes in electricity production. Similarly, rRNA sequences from Firmicutes accounted for 50% of those taxa that increased in relative abundance from current-producing MFCs, implying their functional role in current production. We complemented these analyses by isolating the first organisms from a thermophilic MFC. One of the isolates, a Firmicutes Thermincola sp. strain JR, not only produced more current than known organisms (0.42 mA) in an H-cell system but also represented the first demonstration of direct anode reduction by a member of this phylum. Our research illustrates the importance of using a variety of molecular and culture-based methods to reliably characterize bacterial communities. Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation.

Anaerobic Nitrate-Dependent Iron(II) Bio-Oxidation by a Novel Lithoautotrophic Betaproteobacterium, Strain 2002

ABSTRACT Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)-oxidizing microbial community (2.4 × 103 to 1.5 × 104 cells g−1 wet sediment) from which a novel anaerobic, lithoautotrophic, Fe(II)-oxidizing bacterium, strain 2002, was isolated. Analysis of the complete 16S rRNA gene sequence revealed that strain 2002 was a member of the beta subclass of the proteobacteria with 94.8% similarity to Chromobacterium violaceum, a bacterium not previously recognized for the ability to oxidize nitrate-dependent Fe(II). Under nongrowth conditions, both strain 2002 and C. violaceum incompletely reduced nitrate to nitrite with Fe(II) as the electron donor, while under growth conditions nitrate was reduced to gaseous end products (N2 and N2O). Lithoautotrophic metabolism under nitrate-dependent Fe(II)-oxidizing conditions was verified by the requirement of CO2 for growth as well as the assimilation of 14C-labeled CO2 into biomass. The isolation of strain 2002 represents the first example of an anaerobic, mesophilic, neutrophilic Fe(II)-oxidizing lithoautotroph isolated from freshwater samples. Our studies further demonstrate the abundance of nitrate-dependent Fe(II) oxidizers in freshwater lake sediments and provide further evidence for the potential of microbially mediated Fe(II) oxidation in anoxic environments.

Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY

Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.

Biosignatures link microorganisms to iron mineralization in a paleoaquifer

Concretions, preferentially cemented masses within sediments and sedimentary rocks, are records of sediment diagenesis and tracers of pore water chemistry. For over a century, rinded spheroidal structures that exhibit an Fe(III) oxide–rich exterior and Fe-poor core have been described as oxidation products of Fe(II) carbonate concretions. However, mechanisms governing Fe(III) oxide precipitation within these structures remain an enigma. Here we present chemical and morphological evidence of microbial biosignatures in association with Fe(III) oxides in the Fe(III) oxide–rich rind of spheroidal concretions collected from the Jurassic Navajo Sandstone (southwest United States), implicating a microbial role in Fe biomineralization. The amount of total organic carbon in the exterior Fe(III) oxides exceeded measured values in the friable interior. The mean δ 13 C value of organic carbon from the Fe(III) oxide–cemented exterior, δ 13 C of −20.55‰, is consistent with a biogenic signature from autotrophic bacteria. Scanning electron micrographs reveal microstructures consistent with bacterial size and morphology, including a twisted-stalk morphotype that resembled an Fe(II)-oxidizing microorganism, Gallionella sp. Nanoscale associations of Fe, O, C, and N with bacterial morphotypes demonstrate microorganisms associated with Fe(III) oxides. Together these results indicate that autotrophic microorganisms were present during Fe(III) oxide precipitation and present microbial catalysis as a mechanism of Fe(III) oxide concretion formation. Microbial biosignatures in rinded Fe(III) oxide–rich concretions within an exhumed, Quaternary aquifer has broad implications for detection of life within the geological record on Earth as well as other Fe-rich rocky planets such as Mars, where both Fe(II) carbonate and Fe(III) oxide–rich concretions have been identified.

Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils

ABSTRACT This study demonstrates the prevalence, phylogenetic diversity, and physiology of nitrate-reducing microorganisms capable of utilizing reduced humic acids (HA) as electron donors in agricultural soils. Most probable number (MPN) enumeration of agricultural soils revealed large populations (104 to 106 cells g−1 soil) of microorganisms capable of reducing nitrate while oxidizing the reduced HA analog 2,6-anthrahydroquinone disulfonate (AH2DS) to its corresponding quinone. Nitrate-dependent HA-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. Subsequent 16S rRNA gene-based high-density oligonucleotide microarray (PhyloChip) indicated that reduced HA columns supported the development of a bacterial community enriched with members of the Acidobacteria, Firmicutes, and Betaproteobacteria relative to the no-donor control and initial inoculum. This study identifies a previously unrecognized role for HA in stimulating denitrification processes in saturated soil systems. Furthermore, this study indicates that reduced humic acids impact soil geochemistry and the indigenous bacterial community composition. IMPORTANCE This study identifies a new metabolic capacity in soil microbial communities that may be responsible for the mediation of significant nitrogen losses from soil systems. Nitrate-dependent humic acid (HA)-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. This study identifies a new metabolic capacity in soil microbial communities that may be responsible for the mediation of significant nitrogen losses from soil systems. Nitrate-dependent humic acid (HA)-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups.

Morphologic Clues to the Origins of Iron Oxide–Cemented Spheroids, Boxworks, and Pipelike Concretions, Navajo Sandstone of South-Central Utah, U.S.A.

Concretions cemented by iron oxide are abundant and diverse in the Jurassic Navajo Sandstone of southern Utah. Some of these structures are considered terrestrial analogs for concretions imaged on Mars. The Navajo concretions can be spheroidal, pipelike, or tabular with multicompartmented boxworks. These iron oxide concretions typically display a rinded structure: dense sandstone rinds cemented by iron oxide surround pale, iron-poor sandstone cores. Within a single structure, the iron-rich rinds may be single or multiple. Pseudomorphs of siderite are present in local residual, iron-rich cores of boxworks. Workers in the late nineteenth through mid-twentieth centuries, many of whom found evidence for siderite precusors, concluded that many spherical, rinded, iron oxide-cemented concretions were formed by centripetal precipitation of iron oxide inward from the perimeter of the concretion; in contrast, the walls of pipelike concretions of iron oxide grew centrifugally outward. We interpret the Navajo spheroids and boxworks as centripetal products of the oxidation of siderite-cemented (precursor) concretions that were very similar in both size and shape to the current concretions: rinds grew (thickened) inward toward the internal source of Fe(II). Siderite pseudomorphs appear to be absent from spheroids and many boxworks because all siderite was dissolved. In the cores of the larger boxworks some siderite was oxidized in situ; the Fe(II) did not migrate away from the original siderite crystals. The oxidation process was mediated by iron-oxidizing microbes and began at concretion perimeters when oxidizing groundwater started to displace the CO2- and methane-bearing water that had precipitated the siderite. In contrast, pipelike concretions are centrifugal—rinds formed around a cylindrical reaction front and thickened outward toward Fe(II) and away from the oxygenated water flowing within the cylinders. The cylindrical shape of the reaction front was produced by self-organizing feedbacks between dissolution of dispersed siderite cement and focused flow through a heterogeneous sandstone matrix.

Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002

Pseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic, Fe(II)-oxidizing, nitrate-reducing bacterium. Phylogenetically, it is in a clade within the family Neisseriaceae in the order Nessieriales of the class Betaproteobacteria. It is anticipated that comparative genomic analysis of this strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the elucidation of the genetics and biochemistry underlying this critically important geochemical metabolism.

Environmental and Taxonomic Bacterial Diversity of Anaerobic Uranium(IV) Bio-Oxidation

ABSTRACT Microorganisms in diverse terrestrial surface and subsurface environments can anaerobically catalyze the oxidative dissolution of uraninite. While a limited quantity (∼5 to 12 μmol liter−1) of uranium is oxidatively dissolved in pure culture studies, the metabolism is coupled to electron transport, providing the potential of uraninite to support indigenous microbial populations and to solubilize uranium.

Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with 13C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, 13CO2 production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r2=0.6252, P<0.05) and 13CO2 production (r2=0.6572, P<0.05); whereas change in cell abundance was not correlated to acetate consumption or 13CO2 production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r2=0.5036, P<0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r2=0.5368, P<0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.