Cara M. Santelli

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.

The effect of Fe-oxidizing bacteria on Fe-silicate mineral dissolution

Abstract Acidithiobacillus ferrooxidans are commonly present in acid mine drainage (AMD). A. ferrooxidans derive metabolic energy from oxidation of Fe2+ present in natural acid solutions and also may be able to utilize Fe2+ released by dissolution of silicate minerals during acid neutralization reactions. Natural and synthetic fayalites were reacted in solutions with initial pH values of 2.0, 3.0 and 4.0 in the presence of A. ferrooxidans and in abiotic solutions in order to determine whether these chemolithotrophic bacteria can be sustained by acid-promoted fayalite dissolution and to measure the impact of their metabolism on acid neutralization rates. The production of almost the maximum Fe3+ from the available Fe in solution in microbial experiments (compared to no production of Fe3+ in abiotic controls) confirms A. ferrooxidans metabolism. Furthermore, cell division was detected and the total cell numbers increased over the duration of experiments. Thus, over the pH range 2–4, fayalite dissolution can sustain growth of A. ferrooxidans. However, ferric iron released by A. ferrooxidans metabolism dramatically inhibited dissolution rates by 50–98% compared to the abiotic controls. Two sets of abiotic experiments were conducted to determine why microbial iron oxidation suppressed fayalite dissolution. Firstly, fayalite was dissolved at pH 2 in fully oxygenated and anoxic solutions. No significant difference was observed between rates in these experiments, as expected, due to extremely slow inorganic ferrous iron oxidation rates at pH 2. Experiments were also carried out to determine the effects of the concentrations of Fe2+, Mg2+ and Fe3+ on fayalite dissolution. Neither Fe2+ nor Mg2+ had an effect on the dissolution reaction. However, Fe3+, in the solution, inhibited both silica and iron release in the control, very similar to the biologically mediated fayalite dissolution reaction. Because ferric iron produced in microbial experiments was partitioned into nanocrystalline goethite (with very low Si) that was loosely associated with fayalite surfaces or coated the A. ferrooxidans cells, the decreased rates of accumulation of Fe and Si in solution cannot be attributed to diffusion inhibition by goethite or to precipitation of Fe–Si-rich minerals. The magnitude of the effect of Fe3+ addition (or enzymatic iron oxidation) on fayalite dissolution rates, especially at low extents of fayalite reaction, is most consistent with suppression of dissolution by interaction between Fe3+ and surface sites. These results suggest that microorganisms can significantly reduce the rate at which silicate hydrolysis reactions can neutralize acidic solutions in the environment.

Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction

Manganese (Mn) oxides are among the most reactive minerals within the environment, where they control the bioavailability of carbon, nutrients, and numerous metals. Although the ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides is scattered throughout the bacterial and fungal domains of life, the mechanism and physiological basis for Mn(II) oxidation remains an enigma. Here, we use a combination of compound-specific chemical assays, microspectroscopy, and electron microscopy to show that a common Ascomycete filamentous fungus, Stilbella aciculosa, oxidizes Mn(II) to Mn oxides by producing extracellular superoxide during cell differentiation. The reactive Mn oxide phase birnessite and the reactive oxygen species superoxide and hydrogen peroxide are colocalized at the base of asexual reproductive structures. Mn oxide formation is not observed in the presence of superoxide scavengers (e.g., Cu) and inhibitors of NADPH oxidases (e.g., diphenylene iodonium chloride), enzymes responsible for superoxide production and cell differentiation in fungi. Considering the recent identification of Mn(II) oxidation by NADH oxidase-based superoxide production by a common marine bacterium (Roseobacter sp.), these results introduce a surprising homology between some prokaryotic and eukaryotic organisms in the mechanisms responsible for Mn(II) oxidation, where oxidation appears to be a side reaction of extracellular superoxide production. Given the versatility of superoxide as a redox reactant and the widespread ability of fungi to produce superoxide, this microbial extracellular superoxide production may play a central role in the cycling and bioavailability of metals (e.g., Hg, Fe, Mn) and carbon in natural systems.

The diversity and abundance of bacteria inhabiting seafloor lavas positively correlate with rock alteration.

Young, basaltic ocean crust exposed near mid-ocean ridge spreading centers present a spatially extensive environment that may be exploited by epi- and endolithic microbes in the deep sea. Geochemical energy released during basalt alteration reactions can theoretically support chemosynthesis, contributing to a trophic base for the ocean crust biome. To examine associations between endolithic microorganisms and basalt alteration processes, we compare the phylogenetic diversity, abundance and community structure of bacteria existing in several young, seafloor lavas from the East Pacific Rise at approximately 9 degrees N that are variably affected by oxidative seawater alteration. The results of 16S rRNA gene analyses and real-time, quantitative polymerase chain reaction measurements show that the abundance of prokaryotic communities, dominated by the bacterial domain, positively correlates with the extent of rock alteration--the oldest, most altered basalt harbours the greatest microbial biomass. The bacterial community overlap, structure and species richness relative to alteration state is less explicit, but broadly corresponds to sample characteristics (type of alteration products and general alteration state). Phylogenetic analyses suggest that the basalt biome may contribute to the geochemical cycling of Fe, S, Mn, C and N in the deep sea.

Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities

ABSTRACT Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.

Mn(II)-Oxidizing Bacteria Are Abundant And Environmentally Relevant Members Of Ferromanganese Deposits In Caves Of The Upper Tennessee River Basin

The upper Tennessee River Basin contains the highest density of our nations caves; yet, little is known regarding speleogenesis or Fe and Mn biomineralization in these predominantly epigenic systems. Mn:Fe ratios of Mn and Fe oxide-rich biofilms, coatings, and mineral crusts that were abundant in several different caves ranged from ca. 0.1 to 1.0 as measured using ICP-OES. At sites where the Mn:Fe ratio approached 1.0 this represented an order of magnitude increase above the bulk bedrock ratio, suggesting that biomineralization processes play an important role in the formation of these cave ferromanganese deposits. Estimates of total bacterial SSU rRNA genes in ferromanganese biofilms, coatings, and crusts measured approximately 7×107–9×109 cells/g wet weight sample. A SSU-rRNA based molecular survey of biofilm material revealed that 21% of the 34 recovered dominant (non-singleton) OTUs were closely related to known metal-oxidizing bacteria or clones isolated from oxidized metal deposits. Several different isolates that promote the oxidation of Mn(II) compounds were obtained in this study, some from high dilutions (10–8–10–10) of deposit material. In contrast to studies of caves in other regions, SSU rRNA sequences of Mn-oxidizing bacterial isolates in this study most closely matched those of Pseudomonas, Leptothrix, Flavobacterium, and Janthinobacterium. Combined data from geochemical analyses, molecular surveys, and culture-based experiments suggest that a unique consortia of Mn(II)-oxidizing bacteria are abundant and promoting biomineralization processes within the caves of the upper Tennessee River Basin.

Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.

Tapping the Subsurface Ocean Crust Biosphere: Low Biomass and Drilling-Related Contamination Calls for Improved Quality Controls

Microbial communities inhabiting subseafloor ocean crust were analyzed using culture-dependent and -independent techniques of volcanic basement drill-cores from various locations in the Pacific Ocean. Our results suggest that a low-diversity community of bacteria belonging to the Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes exists in this rocky habitat. Drilling-related contamination was observed, however, identification of these phylotypes was (and will continue to be) beneficial for distinguishing indigenous from contamination-related communities. Due to difficulties in accessing the subseafloor crustal environment, this study further highlights the necessity for innovative approaches in future drilling-based microbiological studies conducted in ocean crust.

Mineralogy Drives Bacterial Biogeography of Hydrothermally Inactive Seafloor Sulfide Deposits

Mid-ocean ridge hydrothermal venting creates sulfide deposits containing gradients in mineralogy, fluid chemistry, and temperature. Even when hydrothermal circulation ceases, sulfides are known to host microbial communities. The relationship between mineralogy and microbial community composition in low-temperature, rock-hosted systems has not been resolved at any spatial scale, local or global. To examine the hypothesis that geochemistry of seafloor deposits is a dominant parameter driving environmental pressure for bacterial communities at low-temperature, the shared community membership, richness, and structure was measured using 16S rRNA gene sequences. The focus of the study was on hydrothermally inactive seafloor deposits from multiple locations within one deposit (e.g., single extinct chimney), within one vent field (intra-vent field), and among globally distributed vent fields from three ocean basins (inter-vent field). Distinct mineral substrates, such as hydrothermally inactive sulfides versus basalts, host different communities at low temperature in spite of close geographic proximity and contact with the same hydrothermally influenced deep-sea water. Furthermore, bacterial communities inhabiting hydrothermally inactive sulfide deposits from geographically distant locations cluster together in community cladograms to the exclusion of other deep-sea substrates and settings. From this study, we conclude that at low temperature, mineralogy was a more important variable determining microbial community composition than geographic factors. Supplemental materials are available for this article. Go to the publishers online edition of Geomicrobiology Journal to view the supplemental file.

Fungal oxidative dissolution of the Mn(II)-bearing mineral rhodochrosite and the role of metabolites in manganese oxide formation.

Microbially mediated oxidation of Mn(II) to Mn(III/IV) oxides influences the cycling of metals and remineralization of carbon. Despite the prevalence of Mn(II)-bearing minerals in nature, little is known regarding the ability of microbes to oxidize mineral-hosted Mn(II). Here, we explored oxidation of the Mn(II)-bearing mineral rhodochrosite (MnCO3 ) and characteristics of ensuing Mn oxides by six Mn(II)-oxidizing Ascomycete fungi. All fungal species substantially enhanced rhodochrosite dissolution and surface modification. Mineral-hosted Mn(II) was oxidized resulting in formation of Mn(III/IV) oxides that were all similar to δ-MnO2 but varied in morphology and distribution in relation to cellular structures and the MnCO3 surface. For four fungi, Mn(II) oxidation occurred along hyphae, likely mediated by cell wall-associated proteins. For two species, Mn(II) oxidation occurred via reaction with fungal-derived superoxide produced at hyphal tips. This pathway ultimately resulted in structurally unique Mn oxide clusters formed at substantial distances from any cellular structure. Taken together, findings for these two fungi strongly point to a role for fungal-derived organic molecules in Mn(III) complexation and Mn oxide templation. Overall, this study illustrates the importance of fungi in rhodochrosite dissolution, extends the relevance of biogenic superoxide-based Mn(II) oxidation and highlights the potential role of mycogenic exudates in directing mineral precipitation.