Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes.

Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22-aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e-pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e-pilins were diverse in length and phylogeny, and included truncated e-pilins in Geobacter spp., as well as longer putative e-pilins in Fe(II)-oxidizing Betaproteobacteria and Zetaproteobacteria.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia.

This study evaluates rates and pathways of methane (CH4 ) oxidation and uptake using 14 C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L-1  day-1 to 117 µmol L-1  day-1 ) compared to other lakes, but are sufficiently high to preclude strong CH4 fluxes to the atmosphere. In addition to aerobic CH4 oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH4 oxidation in Lake Matano's anoxic ferruginous waters. Here, CH4 oxidation proceeds in the apparent absence of oxygen (O2 ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH4 carbon that is assimilated vs. oxidized to carbon dioxide (CO2 ) is high (up to 93%), indicating extensive CH4 conversion to biomass and underscoring the importance of CH4 as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Decrypting the sulfur cycle in oceanic oxygen minimum zones.

Here we present ecophysiological studies of the anaerobic sulfide oxidizers considered critical to cryptic sulfur cycling in oceanic oxygen minimum zones (OMZs). We find that HS- oxidation rates by microorganisms in the Chilean OMZ offshore from Dichato are sufficiently rapid (18 nM h-1), even at HS- concentrations well below 100 nM, to oxidize all sulfide produced during sulfate reduction in OMZs. Even at 100 nM, HS- is well below published half-saturation concentrations and we conclude that the sulfide-oxidizing bacteria in OMZs (likely the SUP05/ARTIC96BD lineage of the gammaproteobacteria) have high-affinity (>105 g-1 wet cells h-1) sulfur uptake systems. These specific affinities for sulfide are higher than those recorded for any other organism on any other substrate. Such high affinities likely allow anaerobic sulfide oxidizers to maintain vanishingly low sulfide concentrations in OMZs driving marine cryptic sulfur cycling. If more broadly distributed, such high-affinity sulfur biochemistry could facilitate sulfide-based metabolisms and prominent S-cycles in many other ostensibly sulfide-free environments.

Oxidative elemental cycling under the low O2 Eoarchean atmosphere.

The Great Oxidation Event signals the first large-scale oxygenation of the atmosphere roughly 2.4 Gyr ago. Geochemical signals diagnostic of oxidative weathering, however, extend as far back as 3.3-2.9 Gyr ago. 3.8-3.7 Gyr old rocks from Isua, Greenland stand as a deep time outpost, recording information on Earth's earliest surface chemistry and the low oxygen primordial biosphere. Here we find fractionated Cr isotopes, relative to the igneous silicate Earth reservoir, in metamorphosed banded iron formations (BIFs) from Isua that indicate oxidative Cr cycling 3.8-3.7 Gyr ago. Elevated U/Th ratios in these BIFs relative to the contemporary crust, also signal oxidative mobilization of U. We suggest that reactive oxygen species were present in the Eoarchean surface environment, under a very low oxygen atmosphere, inducing oxidative elemental cycling during the deposition of the Isua BIFs and possibly supporting early aerobic biology.

Sulfate was a trace constituent of Archean seawater.

In the low-oxygen Archean world (>2400 million years ago), seawater sulfate concentrations were much lower than today, yet open questions frustrate the translation of modern measurements of sulfur isotope fractionations into estimates of Archean seawater sulfate concentrations. In the water column of Lake Matano, Indonesia, a low-sulfate analog for the Archean ocean, we find large (>20 per mil) sulfur isotope fractionations between sulfate and sulfide, but the underlying sediment sulfides preserve a muted range of δ(34)S values. Using models informed by sulfur cycling in Lake Matano, we infer Archean seawater sulfate concentrations of less than 2.5 micromolar. At these low concentrations, marine sulfate residence times were likely 10(3) to 10(4) years, and sulfate scarcity would have shaped early global biogeochemical cycles, possibly restricting biological productivity in Archean oceans.

Surface chemistry allows for abiotic precipitation of dolomite at low temperature.

Although the mineral dolomite is abundant in ancient low-temperature sedimentary systems, it is scarce in modern systems below 50 °C. Chemical mechanism(s) enhancing its formation remain an enigma because abiotic dolomite has been challenging to synthesize at low temperature in laboratory settings. Microbial enhancement of dolomite precipitation at low temperature has been reported; however, it is still unclear exactly how microorganisms influence reaction kinetics. Here we document the abiotic synthesis of low-temperature dolomite in laboratory experiments and constrain possible mechanisms for dolomite formation. Ancient and modern seawater solution compositions, with identical pH and pCO2, were used to precipitate an ordered, stoichiometric dolomite phase at 30 °C in as few as 20 d. Mg-rich phases nucleate exclusively on carboxylated polystyrene spheres along with calcite, whereas aragonite forms in solution via homogeneous nucleation. We infer that Mg ions are complexed and dewatered by surface-bound carboxyl groups, thus decreasing the energy required for carbonation. These results indicate that natural surfaces, including organic matter and microbial biomass, possessing a high density of carboxyl groups may be a mechanism by which ordered dolomite nuclei form. Although environments rich in organic matter may be of interest, our data suggest that sharp biogeochemical interfaces that promote microbial death, as well as those with high salinity may, in part, control carboxyl-group density on organic carbon surfaces, consistent with origin of dolomites from microbial biofilms, as well as hypersaline and mixing zone environments.

Stable isotopes reveal widespread anaerobic methane oxidation across latitude and peatland type.

Peatlands are an important source of the atmospheric greenhouse gas methane (CH4). Although CH4 cycling and fluxes have been quantified for many northern peatlands, imprecision in process-based approaches to predicting CH4 emissions suggests that our understanding of underlying processes is incomplete. Microbial anaerobic oxidation of CH4 (AOM) is an important CH4 sink in marine sediments, but AOM has only recently been identified in a few nonmarine systems. We used (13)C isotope tracers and followed the fate of (13)C into CO2 and peat in order to study the geographic extent, relative importance, and biogeochemistry of AOM in 15 North American peatlands spanning a ∼1500 km latitudinal transect that varied in hydrology, vegetation, and soil chemistry. For the first time, we demonstrate that AOM is a widespread and quantitatively important process across many peatland types and that anabolic microbial assimilation of CH4-C occurs. However, AOM rate is not predicted by CH4 production rates and the primary mechanism of C assimilation remains uncertain. AOM rates are higher in fen than bog sites, suggesting electron acceptor constraints on AOM. Nevertheless, AOM rates were not correlated with porewater ion concentrations or stimulated following additions of nitrate, sulfate, or ferric iron, suggesting that an unidentified electron acceptor(s) must drive AOM in peatlands. Globally, we estimate that AOM could consume a large proportion of CH4 produced annually (1.6-49 Tg) and thereby constrain emissions and greenhouse gas forcing.

Photoferrotrophs thrive in an Archean Ocean analogue.

Considerable discussion surrounds the potential role of anoxygenic phototrophic Fe(II)-oxidizing bacteria in both the genesis of Banded Iron Formations (BIFs) and early marine productivity. However, anoxygenic phototrophs have yet to be identified in modern environments with comparable chemistry and physical structure to the ancient Fe(II)-rich (ferruginous) oceans from which BIFs deposited. Lake Matano, Indonesia, the eighth deepest lake in the world, is such an environment. Here, sulfate is scarce (<20 micromol x liter(-1)), and it is completely removed by sulfate reduction within the deep, Fe(II)-rich chemocline. The sulfide produced is efficiently scavenged by the formation and precipitation of FeS, thereby maintaining very low sulfide concentrations within the chemocline and the deep ferruginous bottom waters. Low productivity in the surface water allows sunlight to penetrate to the >100-m-deep chemocline. Within this sulfide-poor, Fe(II)-rich, illuminated chemocline, we find a populous assemblage of anoxygenic phototrophic green sulfur bacteria (GSB). These GSB represent a large component of the Lake Matano phototrophic community, and bacteriochlorophyll e, a pigment produced by low-light-adapted GSB, is nearly as abundant as chlorophyll a in the lake's euphotic surface waters. The dearth of sulfide in the chemocline requires that the GSB are sustained by phototrophic oxidation of Fe(II), which is in abundant supply. By analogy, we propose that similar microbial communities, including populations of sulfate reducers and photoferrotrophic GSB, likely populated the chemoclines of ancient ferruginous oceans, driving the genesis of BIFs and fueling early marine productivity.

Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources.

Methane is a major greenhouse gas linked to global warming; however, patterns of in situ methane oxidation by methane-oxidizing bacteria (methanotrophs), nature's main biological mechanism for methane suppression, are often inconsistent with laboratory predictions. For example, one would expect a strong relationship between methanotroph ecology and Cu level because methanotrophs require Cu to sustain particulate methane monooxygenase (pMMO), the most efficient enzyme for methane oxidation. However, no correlation has been observed in nature, which is surprising because methane monooxygenase (MMO) gene expression has been unequivocally linked to Cu availability. Here we provide a fundamental explanation for this lack of correlation. We propose that MMO expression in nature is largely controlled by solid-phase Cu geochemistry and the relative ability of Cu acquisition systems in methanotrophs, such as methanobactins (mb), to obtain Cu from mineral sources. To test this hypothesis, RT-PCR expression assays were developed for Methylosinus trichosporium OB3b (which produces mb) to quantify pMMO, soluble MMO (the alternate MMO expressed when Cu is "unavailable"), and 16S-rRNA gene expression under progressively more stringent Cu supply conditions. When Cu was provided as CuCl(2), pMMO transcript levels increased significantly consistent with laboratory work. However, when Cu was provided as Cu-doped iron oxide, pMMO transcript levels increased only when mb was also present. Finally, when Cu was provided as Cu-doped borosilicate glass, pMMO transcription patterns varied depending on the ambient mb:Cu supply ratio. Cu geochemistry clearly influences MMO expression in terrestrial systems, and, as such, local Cu mineralogy might provide an explanation for methane oxidation patterns in the natural environment.

Microbial selenate sorption and reduction in nutrient limited systems.

In this study, batch sorption experiments and X-ray adsorption spectroscopy (XAS) were utilized to investigate selenate sorption onto Shewanella putrefaciens 200R. Selenate sorption was studied as a function of pH (ranging from 3 to 7), ionic strength (ranging from 0.1 to 0.001 M), and initial selenate concentration (ranging from 10 to 5000 microM) in the absence of external electron donors. The results show that the extent of selenate sorption is strongly dependent on pH and ionic strength, with maximum sorption occurring at low pH (pH = 3) and low ionic strength (0.001 M NaCl) conditions. The strong dependence of Se sorption with ionic strength suggests the formation of outersphere complexes with the cell wall functional groups. Langmuir isotherm plots yielded log Kads values from 2.74 to 3.02. Desorption experiments demonstrated thatthe binding of selenate onto S. putrefaciens was not completely reversible. XANES analysis of the cells after sorption experiments revealed the presence of elemental selenium, indicating that S. putrefaciens has a capacity to reduce Se(VI) to Se(0) in the absence of external electron donors. We conclude that Se sorption onto S. putrefaciens cell walls is the result of the combination of outer-sphere complexation and cell surface reduction. This sorption process leads to a complex reservoir of bound Se which is not entirely reversible.