Katrina J. Edwards

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

SUMMARY The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

Abundance and diversity of microbial life in ocean crust

Oceanic lithosphere exposed at the sea floor undergoes seawater–rock alteration reactions involving the oxidation and hydration of glassy basalt. Basalt alteration reactions are theoretically capable of supplying sufficient energy for chemolithoautotrophic growth. Such reactions have been shown to generate microbial biomass in the laboratory, but field-based support for the existence of microbes that are supported by basalt alteration is lacking. Here, using quantitative polymerase chain reaction, in situ hybridization and microscopy, we demonstrate that prokaryotic cell abundances on seafloor-exposed basalts are 3–4 orders of magnitude greater than in overlying deep sea water. Phylogenetic analyses of basaltic lavas from the East Pacific Rise (9° N) and around Hawaii reveal that the basalt-hosted biosphere harbours high bacterial community richness and that community membership is shared between these sites. We hypothesize that alteration reactions fuel chemolithoautotrophic microorganisms, which constitute a trophic base of the basalt habitat, with important implications for deep-sea carbon cycling and chemical exchange between basalt and sea water.

Iron and sulfide oxidation within the basaltic ocean crust: Implications for chemolithoautotrophic microbial biomass production

Microbial processes within the ocean crust are of potential importance in controlling rates of chemical reactions and thereby affecting chemical exchange between the oceans and lithosphere. We here assess the oxidation state of altered ocean crust and estimate the magnitude of microbial biomass production that might be supported by oxidative and nonoxidative alteration. Compilations of Fe2O3, FeO, and S concentrations from DSDP/ODP drill core samples representing upper basaltic ocean crust suggest that Fe3+/ΣFe increases from 0.15 ± 0.05 to 0.45 ± 0.15 within the first 10–20 Myr of crustal evolution. Within the same time frame 70 ± 25% of primary sulfides in basalt are oxidized. With an annual production of 4.0 ± 1.8 × 1015 g of upper (500 ± 200 m) crust and average initial concentrations of 8.0 ± 1.3 wt% Fe and 0.125 ± 0.020 wt% S, we estimate annual oxidation rates of 1.7 ± 1.2 × 1012 mol Fe and 1.1 ± 0.7 × 1011 mol S. We estimate that 50% of Fe oxidation may be attributed to hydrolysis, producing 4.5 ± 3.0 × 1011 mol H2/yr. Thermodynamic and bioenergetic calculations were used to estimate the potential chemolithoautotrophic microbial biomass production within ridge flanks. Combined, aerobic and anaerobic Fe and S oxidation may support production of up to 48 ± 21 × 1010 g cellular carbon (C). Hydrogen-consuming reactions may support production of a similar or larger microbial biomass if iron reduction, nitrate reduction, or hydrogen oxidation by O2(aq) are the prevailing metabolic reactions. If autotrophic sulfate reduction or methanogenesis prevail, the potential biomass production is 9 ± 7 × 1010 g C/yr and 3 ± 2 × 1010 g C/yr, respectively. Combined primary biomass production of up to ∼1 × 1012 g C/yr may be similar to that fueled by anaerobic oxidation of organic matter in deep-seated heterotrophic systems. These estimates suggest that water-rock reactions may support significant microbial life within ridge flank hydrothermal systems, These estimates suggest that water-rock reactions may support significant microbial life within ridge flank hydrothermal systems.

Isolation and Characterization of Novel Psychrophilic, Neutrophilic, Fe-Oxidizing, Chemolithoautotrophic α- and γ-Proteobacteria from the Deep Sea

ABSTRACT We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS2), basalt glass (∼10 wt% FeO), and siderite (FeCO3), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10°C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are γ-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are α-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalks metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h−1). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

Spatiotemporal Distribution of Marine Magnetotactic Bacteria in a Seasonally Stratified Coastal Salt Pond

ABSTRACT The occurrence and distribution of magnetotactic bacteria (MB) were studied as a function of the physical and chemical conditions in meromictic Salt Pond, Falmouth, Mass., throughout summer 2002. Three dominant MB morphotypes were observed to occur within the chemocline. Small microaerophilic magnetite-producing cocci were present at the top of the chemocline, while a greigite-producing packet-forming bacterium occurred at the base of the chemocline. The distributions of these groups displayed sharp changes in abundance over small length scales within the water column as well as strong seasonal fluctuations in population abundance. We identified a novel, greigite-producing rod in the sulfidic hypolimnion that was present in relatively constant abundance over the course of the season. This rod is the first MB that appears to belong to the γ-Proteobacteria, which may suggest an iron- rather than sulfur-based respiratory metabolism. Its distribution and phylogenetic identity suggest that an alternative model for the ecological and physiological role of magnetotaxis is needed for greigite-producing MB.

Geomicrobiology of Pyrite (FeS2) Dissolution: Case Study at Iron Mountain, California

Geomicrobiology of pyrite weathering at Iron Mountain, CA, was investigated by molecular biological, surface chemical, surface structural, and solution chemical methods in both laboratory and field-based studies. Research focused at sites both within and peripheral to the ore-body. The acid-generating areas we have examined thus far at Iron Mountain (solution pH 35 C) were populated by species other than Thiobacillus ferrooxidans . 16S rDNA bacterial sequence analysis and domain- and specieslevel oligonucleotide probe-based investigations confirmed the presence of planktonic Leptospirillum ferrooxidans and indicated the existence of other species apparently related to other newly described acidophilic chemolithotrophs. T. ferrooxidans was confined to relatively moderate environments (pH 2-3, 20-30 C) that were peripheral to the orebody. Dissolution rate measurements indicated that, per cell, attached and planktonic species contributed comparably in acid release. Surface colonizati...

Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats, Diversity, and Roles in Mineral Deposition, Rock Alteration, and Biomass Production in the Deep-Sea

The importance of metals to life has long been appreciated. Iron (Fe) is the fourth most abundant element overall, and the second most abundant element that is redox-active in near-surface aqueous habitats, rendering it the most important environmental metal. While it has long been recognized that microorganisms participate in the global iron cycle, appreciation for the pivotal role that redox cycling of iron plays in energy conservation among diverse prokaryotes has grown substantially in the past decade. In addition, redox reactions involving Fe are linked to several other biogeochemical cycles (e.g., carbon), with significant ecological ramifications. The increasing appreciation for the role of microbes in redox transformations of Fe is reflected in a recent surge in biological and environmental studies of microorganisms that conserve energy for growth from redox cycling of Fe compounds, particularly in the deep ocean. Here we highlight some of the key habitats where microbial Fe-oxidation plays significant ecological and biogeochemical roles in the oceanic regime, and provide a synthesis of recent studies concerning this important physiological group. We also provide the first evidence that microbial Fe-oxidizing bacteria are a critical factor in the kinetics of mineral dissolution at the seafloor, by accelerating dissolution by 6–8 times over abiotic rates. We assert that these recent studies, which indicate that microbial Fe-oxidation is widespread in the deep-sea, combined with the apparent role that this group play in promoting rock and mineral weathering, indicate that a great deal more attention to these microorganisms is warranted in order to elucidate the full physiological and phylogenetic diversity and activity of the neutrophilic Fe-oxidizing bacteria in the oceans.

Geochemical and biological aspects of sulfide mineral dissolution: lessons from Iron Mountain, California

Abstract The oxidative dissolution of sulfide minerals leading to acid mine drainage (AMD) involves a complex interplay between microorganisms, solutions, and mineral surfaces. Consequently, models that link molecular level reactions and the microbial communities that mediate them to field scale processes are few. Here we provide a mini-review of laboratory and field-based studies concerning the chemical, microbial, and kinetic aspects of sulfide mineral dissolution and generation of AMD at the Richmond ore body at Iron Mountain, California.

Seafloor bioalteration of sulfide minerals: Results from in situ incubation studies

We present results of incubation studies conducted at low temperatures (∼4°C) in the vicinity of a seafloor hydrothermal vent system. We reacted Fe-, S-, Cu-, and Zn-bearing minerals including pyrite, marcasite, chalcopyrite, sphalerite, elemental sulfur, and a portion of a natural chimney sulfide structure for 2 months at the Main Endeavour Segment of the Juan de Fuca Ridge in the Pacific Ocean. Our study utilizes Fluorescent In Situ Hybridizations (FISH), Scanning and Transmission Electron Microscopy (SEM, TEM), and light microscopic analysis. The surfaces of these minerals are solely colonized by Bacteria and not by Archaea. Colonization densities vary over an order of magnitude with the following sequence: elemental sulfur > chimney sulfide > marcasite > pyrite > sphalerite > chalcopyrite, and correspond well with the abiotic oxidation kinetics of these materials, excepting elemental sulfur, which is both the least reactive to oxidizing species and the most heavily colonized. Colonization densities also correspond with apparent degree of reaction (dissolution pitting + accumulation of secondary alteration products). Heavy accumulations of secondary Fe oxides on Fe-bearing minerals, most notably on the chimney sulfide, form in situ as the result of mineral dissolution and the activity of neutrophilic Fe-oxidizing bacteria. Results suggest that mineral-oxidizing bacteria play a prominent role in weathering of seafloor sulfide deposits, and that microbial utilization of mineral substrates contributes to biomass production in seafloor hydrothermal environments.