Self-potential time series reveal emergent behavior in soil organic matter dynamics.

The active cycling of carbon between soil organic matter and the atmosphere is of critical importance to global climate change. An extensive body of research exists documenting the capricious nature of soil organic matter (SOM) dynamics, which is symptomatic of an intricate network of interactions between diverse groups of heterotrophic microorganisms, complex organic substrates, and highly variable local environmental conditions. These attributes are consistent with elements of complex system theory and the temporal evolution of otherwise unpredictable patterns of behavior that emerge from long range dependency on initial conditions. Here we show that vertical depth profile of self-potential (SP) time series measurements responds in a quantitative manner to variations in soil moisture, SOM concentrations, and relative rates of microbial activity. Application of detrended fluctuation analysis (DFA) of self potential time series data is shown additionally to reveal the presence of long-range dependence and emergence of anomalous electrochemical diffusion behavior, both of which diminish with depth as SOM specific energy densities decline.

Long Range Correlation in Redox Potential Fluctuations Signals Energetic Efficiency of Bacterial Fe(II) Oxidation.

Differentiating biotic and abiotic processes in nature remains a persistent challenge, specifically in evaluating microbial contributions to geochemical processes through time. Building on previous work reporting that biologically-influenced systems exhibit stronger long-range correlation than abiotic systems, this study evaluated the relationship between long-range correlation of redox potential and oxidation rates of circumneutral microaerophilic bacterial Fe(II) oxidation using a series of batch microcosms with bacteriogenic iron oxides (BIOS). Initial detrended fluctuation analysis (DFA) scaling exponents of the abiotic microcosms were lower (ca. 1.20) than those of the biotic microcosms (ca. 1.80). As Fe(II) oxidation proceeded, correlation strength decayed as a logistic function of elapsed reaction time, exhibiting direct dependence on the free energy of reaction. Correlation strength for all microcosms decayed sharply from strong correlation to uncorrelated fluctuations. The decay rates are greater for abiotic microcosms than biotic microcosms. The ΔGm relaxation edges for biotic microcosms were lower, indicating less remaining free energy for Fe(II) oxidation than abiotic systems, with the implication that biologically-catalyzed reactions are likely more energetically efficient than abiotic reactions. These results strengthen the case for employing novel DFA techniques to distinguish in situ microbial metabolic activity from abiotic processes, as well as to potentially differentiate metabolisms among different chemoautotrophs.

Sorption of strontium onto bacteriogenic iron oxides.

Bacteriogenic iron oxides (BIOS) were obtained from a dilute, circumneutral groundwater seep, characterized with respect to mineralogy, and examined for their ability to sorb aqueous Sr2+. BIOS were composed of microbial sheaths encrusted in 2-line ferrihydrite. Sorption experiments indicated that Sr remained completely unbound at pH < 4.5, but sorption increased with increasing pH (maximum of 95% at pH > 7.6). EXAFS analysis of Sr-loaded BIOS failed to elucidate whether Sr sorption occurred on sites specific to the mineral or microbial fraction, but indicated that sorption likely occurred by outer-sphere complexation between BIOS and hydrated Sr2+. Sorption experiments showed that at low ionic strength (I = 0.001 M), sorption followed a Langmuir isotherm (S(max) = 3.41 mol Sr (g of Fe)(1-), K(ads) = 1.26). At higher ionic strength (I = 0.1 M), there was significant inhibition of Sr sorption (S(max) = 1.06 mol Sr (g of Fe)(1-), K(ads) = 1.23), suggesting that sorption to BIOS occurs by outer-sphere complexation. The results suggest that, under dilute circumneutral conditions, BIOS deposits should efficiently sorb dissolved Sr from groundwater flow systems where such deposits exist. This finding has particular relevance to sites impacted by radioactive 90Sr groundwater contamination.

Viruses in granitic groundwater from 69 to 450 m depth of the Aspö hard rock laboratory, Sweden.

The objectives of this study were to determine if viruses exist in deep granitic groundwater and to analyse their abundance and morphological diversity. Fluorescent microscopy counts on 10 groundwater samples ranging from 69 to 450 m depth were in the range of 10(4)-10(6) TNC ml(-1) (TNC, total number of prokaryotic cells) and 10(5)-10(7) VLP ml(-1) (VLP, virus-like particles). A good positive correlation of VLP with TNC (r=0.91, P=0.0003) was found with an average VLP/TNC ratio of 12. Transmission electron microscopy revealed four distinct bacteriophage groups (polyhedral, tailed, filamentous and pleomorphic) with at least seven phage families of which some are known to be lytic. Our results suggest the presence of viruses in deep granitic groundwater up to 450 m depth. If they are active and lytic, they will constitute an important group of predators that might control the numbers of microorganisms in the analysed groundwater.

Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats.

Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.

Effect of strontium contaminants upon the size and solubility of calcite crystals precipitated by the bacterial hydrolysis of urea.

The nucleation and growth of calcite precipitates induced by the bacterial hydrolysis of urea (ureolysis) from a Sr-contaminant inclusive, and a Sr-free artificial groundwater (AGW) mimicking the composition of the 90Sr contaminated Snake River Plain aquifer were investigated. Sr-free experiments exhibited a gradual increase in mean calcite crystal diameter (<1000 nm) from day (D) 1 to 6, while in the Sr-inclusive experiments, daily diameters were approximately constant from D1 to D6, and crystals were smaller (mean <840 nm). These data demonstrate a steady state had been attained early in the Sr-inclusive experiments from growth inhibition by Sr. Modeling of the crystal growth mechanisms on the USGS GALOPER software suggested crystal size distributions in the Sr-inclusive and Sr-free experiments were generated in the nucleation stage by a decreasing nucleation rate with surface-controlled growth, followed by supply-controlled and random growth. This occurred despite the availability of Ca2+ and HCO3-, implying crystal growth is limited bythe rate of solute advection to the crystal surface. Calculation of the solubility constant (In KsO(A)) demonstrates smaller crystals are more soluble, reflecting a higher molar surface area. The coprecipitation of Sr therefore generates smaller and thus more soluble crystals. However, this is unlikely to dramatically reduce the long-term effectiveness of Sr immobilization because when crystal growth had ceased in the Sr-inclusive AGW, > 99% of calcite precipitated and Sr coprecipitated occurred in large crystals with a low solubility.

Cadmium complexation by bacteriogenic iron oxides from a subterranean environment.

This study quantifies the metal sorption characteristics of subterranean bacteriogenic iron oxides (BIOS) and their organic phases (intermixed intact and fragmented bacteria). A Cd2+ ion-selective electrode was used to generate high-resolution metal sorption data as a function of increasing pH. A multisite Langmuir model, along with a linear programming regression method (LPM), was applied to fit experimental data. This approach found two discrete Cd2+ binding sites for the BIOS with average -log10 equilibrium constants (pK(S,j)) of 1.06 +/- 0.19 and 2.24 +/- 0.28. Three discrete sites were obtained for the bacterial fraction, with pK(S,j) values of -0.05 +/- 0.12, 1.18 +/- 0.02, and 3.81 +/- 0.16. This indicated that the BIOS surface had a lower affinity for Cd2+ than that of the bacteria. pK(S,j) values for the BIOS were similar to those reported for pure iron oxide phases, while the organic fraction pK(S,j) spectrum was consistent with previous spectra for intact bacteria. Individual binding site densities of 0.04 +/- 0.01 and 0.05 +/- 0.02 and 0.29 +/- 0.05, 0.11 +/- 0.01, and 0.09 +/- 0.02 micromol/mg of BIOS corresponded to the iron oxide mixture and bacteria fraction, respectively. These values indicated high concentrations of strong affinity Cd2+ complexing groups on the bacterial surface. Comparison of total site densities of 0.08 +/- 0.02 and 0.48 +/- 0.06 micromol/mg of BIOS for the mixture and the bacterial phase, respectively, suggested a nonadditive character for the BIOS surface reactivity. This was emphasized by a higher affinity for Cd2+, as well as an increase in total site concentration observed for the bacterial phase. LPM was able to distinguish between the BIOS mixture and its organic fraction Cd2+ complexation characteristics. This approach is therefore a useful tool for the study of natural sorbent materials controlling metal partitioning in contaminated and pristine environments.

Characterization of metal-cyanobacteria sorption reactions: a combined macroscopic and infrared spectroscopic investigation.

In this study, we conducted synchrotron radiation Fourier transform infrared (IR) spectroscopy, potentiometric titration, and metal sorption experiments to characterize metal-cyanobacteria sorption reactions. Infrared spectra were collected with samples in solution for intact cyanobacterial filaments and separated exopolymeric sheath material to examine the deprotonation reactions of cell surface functional groups. The infrared spectra of intact cells sequentially titrated from pH 3.2 to 6.5 display an increase in peak intensity and area at 1400 cm(-1) corresponding to vibrational COO- frequencies from the formation of deprotonated carboxyl surface sites. Similarly, bulk acid-base titration of cyanobacterial filaments and sheath material indicates that the concentration of proton-active surface sites is higher on the cell wall compared to the overlying sheath. A three-site model provides an excellent fit to the titration curves of both intact cells and sheath material with corresponding pKa values of 4.7 +/- 0.4, 6.6 +/- 0.2, 9.2 +/- 0.3 and 4.8 +/- 0.3, 6.5 +/- 0.1, 8.7 +/- 0.2, respectively. Finally, Cu2+, Cd2+, and Pb2+ sorption experiments were conducted as a function of pH, and a site-specific surface complexation model was used to describe the metal sorption data. The modeling indicates that metal ions are partitioned between the exopolymer sheath and cell wall and that the carboxyl groups on the cyanobacterial cell wall are the dominant sink for metals at near neutral pH. These results demonstrate that the cyanobacterial surfaces are complex structures which contain distinct surface layers, each with unique molecular functional groups and metal binding properties.

Specific surface chemical interactions between hydrous ferric oxide and iron-reducing bacteria determined using pK(a) spectra.

A modified regularized least squares pK(a) spectrum approach is applied to determine disassociation constants and proton binding site concentrations on bacteria, hydrous ferric oxide (HFO), and bacteria/HFO composite surfaces. This involves fitting experimental acid-base titration data to a continuous binding site model for a chemically heterogeneous surface with a variety of reactive groups yielding a pK(a) spectrum. The modified parameter fitting method optimizes simultaneously for both smoothness of the pK(a) spectrum and goodness of fit, whereas other methods optimize for goodness of fit given a fixed smoothness factor. Uncertainty estimates in pK(a) spectra were made by taking the mean and standard deviation of the spectra from replicate titration data. Titration of Shewanella putrefaciens strain CN32, a facultative iron-reducing bacterial species, demonstrate five types of binding sites consistent with known cell surface groups on bacteria, with mean pK(a) values of 3.62, 4.97, 6.92, 8.22, and 9.97. Composite surfaces formed by precipitation of HFO onto bacteria surfaces were also titrated. These surfaces no longer yielded low pK(a) sites in pK(a) spectra, indicating that ferric iron interacts with the bacteria via carboxylic (low pK(a)) sites during precipitation. In addition, mechanically mixed HFO bacterial samples also showed removal of carboxylic binding sites, suggesting that solid phase HFO interacts directly with carboxylic sites on bacterial cells. Moreover, the pK(a) spectra for HFO bacterial composites were not dependent on how the composite was formed; the mechanically mixed or surface-precipitated samples exhibited very similar binding site distributions. The determined pK(a) spectra imply that the overall binding mechanism for bacteria interactions with HFO involve carboxylic groups on the bacteria binding to the most basic sites on the HFO surface in approximately 1:1 stoichiometry.

Surface chemical heterogeneity of bacteriogenic iron oxides from a subterranean environment.

This study quantifies the surface chemical heterogeneity of bacteriogenic iron oxides (BIOS) and its end-members (2-line ferrihydrite and intermixed intact and fragmented bacteria). On a dry weight basis, BIOS consisted of 64.5 +/- 1.8% ferrihydrite and 34.5 +/- 1.8% organic matter. Enrichment of Al, Cu, Cr, Mn, Sr, and Zn was shown in the solid versus the aqueous phase (1.9 < log Kd < 4.2). Within the solid-phase Al (69.5%), Cu (78.7%), and Zn (77.9%) were associated with the bacteria, whereas Cr (59.8%), Mn (99.8%), and Sr (79.4%) preferred ferrihydrite. Acid-base titration data from the BIOS and bacteria were fitted using FOCUS pKa spectroscopy. The bacteria spectrum with pKa's of 4.18 +/- 0.37, 4.80 +/- 0.54, 6.98 +/- 0.45, and 9.75 +/- 0.68 was similar to discrete and continuous spectra for intact and fragmented bacteria. The BIOS spectrum recorded pKa's of 4.27 +/- 0.51, 6.61 +/- 0.51, 7.89 +/- 1.10, and 9.65 +/- 0.66 and was deconvoluted to remove overlapping binding site contributions from the bacteria. The resulting residual iron oxide spectrum coincided with discrete MUSIC spectra for goethite and lepidocrocite with pKa values of 4.10 +/- 0.43, 6.53 +/- 0.45, 7.81 +/- 0.76, and 9.51 +/- 0.68. Surface site density analysis showed that acidic sites (pKa < 6) were contributed by the bacteria (37%), whereas neutral sites (6 < pKa < 8) were characteristic of the iron oxide fraction (35%). Basic sites (8 < pKa) were higher in the bacteria (57%), than in the BIOS (44%) or iron oxide fractions (47%). This analysis suggested a high degree of bacterial group masking and a similarity between the BIOS and goethite surface reactivity. An understanding of the BIOS surface chemical heterogeneity and inherent proton and metal binding capacity was obtained through the use of FOCUS apparent pKa spectroscopy.

Determination of intrinsic bacterial surface acidity constants using a donnan shell model and a continuous pK(a) distribution method.

Intrinsic acidity constants (pK(a)(int)) for Bacillus subtilis (Gram+) and Escherichia coli (Gram-) cells were calculated from potentiometric titration data at different salt concentrations. Master curves were generated by replotting charge excess data as a function of pH(S) (pH at the location of surface reactive sites) where pH(S) was determined as a function of Donnan potential, Psi(DON). This potential decreased in magnitude with increasing ionic strength, from -48.5+/-0.2 to -3.5+/-0.0 mV for B. subtilis and -47.9+/-0.3 to -3.5+/-0.0 mV for E. coli at 0.01 and 0.5 M K(+), respectively, indicating an efficient surface charge neutralization by counterions. A fully optimized continuous (FOCUS) pK(a) distribution method revealed four binding sites on B. subtilis and E. coli surfaces from the master curves with pK(a)(int) values of 3.59+/-0.38, 4.33+/-0.57, 5.94+/-0.66, and 8.64+/-0.57 for B. subtilis and 3.73+/-0.44, 4.85+/-0.71, 6.56+/-0.64, and 8.79+/-0.62 for E. coli. These were assigned to functional groups according to reported pK(a) ranges of 2.0-6.0 (carboxylic acid), 3.2-3.5 (phosphodiesters), 5.6-7.2 (phosphoric acid), and 9.0-11.0 (amine groups). Average points of zero salt effect (pH(pzse)) for B. subtilis experiments were 6.63+/-0.21 and 6.42+/-0.08 as a function of pH(bulk) and pH(S), respectively. Under the same criteria, E. coli calculations yielded 5.73+/-0.23 and 5.45+/-0.05. An understanding of metal and proton reactivity on bacterial cell surfaces can be addressed quantitatively through the use of electrostatic and chemical equilibrium modeling techniques proposed in this study. The results are consistent with those of electrical force microscopy studies used to document the intrinsic electrochemical heterogeneity of bacterial cell surfaces.