Solubilization and speciation of iron during pyrite oxidation by Thiobacillus ferrooxidans

Various species of soluble iron in pyrite‐grown cultures of Thiobacillus ferrooxidans were determined by colorimetry, atomic absorption spectrometry, and ultraviolet spectroscopy. All the cultures were incubated for six weeks before iron analysis. The effects of the following factors were investigated: particle size, initial pH, shaking (aeration), concentration of pyrite, and concentration of yeast extract. Shaking, but not initial pH nor particle size, influenced the relative proportion of different iron species. Polynomial regressions could be used to describe the functional relationship between the different iron species and concentration of pyrite; fewer relationships were evident with respect to concentration of yeast extract. The variance‐covariance matrices indicated a linear dependence among the different iron species. Canonical correlations indicated perfect correlations between group variables of iron, copper, and zinc, with the exception of an absence of significant correlation with the hydroxy complex of iron (FeOH²⁺).

The dissolved ferrous iron (dissociated and weakly chelated) always remained less than 7% of the total iron in solution. The total ferrous iron, which included complexed species, amounted to 7–34% of the total iron in solution. The concentrations of dissociated ferrous and ferric iron and their weak chelates (the dissolved iron) remained mostly constant, irrespective of the concentration of the total iron in solution. Most of the total iron was complexed as ferric species and the amount correlated with culture conditions. The hydroxy complex (FeOH²⁺), which was indicative of the relative amount of hydrolyzable ferric iron upon dilution in CO₂‐free water, usually ranged between 60 and 80% of the total iron. The amount of the total iron in uninoculated controls was less than 12% of that solu‐bilized in the presence of iron‐oxidizing thiobacilli.

T. ferrooxidans was enumerated by a most‐probable‐number technique after three and six weeks of growth on pyrite. The counts after three weeks indicated an increase in the number of free and loosely attached bacteria, followed by a decline of about one order of magnitude in bacterial numbers after six weeks. The technique for bacterial enumeration was deemed unsatisfactory because it could not account for cells attached on pyrite.     

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

Pyrite (FeS₂) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro‐organisms in pyrite oxidation under acidic‐pH conditions is well known, to date there is very little known about the capacity for aerobic micro‐organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite‐bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin–Benson–Bassham CO₂ fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30–50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X‐ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro‐organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral‐pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite‐associated metals.     

Pyrite oxidation in acid sulphate soils: The role of miroorganisms

Summary A study has been made of microbial processes in the oxidation of pyrite in aicd sulphate soil material. Such soils are formed during aeration of marine muds rich in pyrite (FeS₂). Bacteria of the type ofThiobacillus ferrooxidans are mainly responsible for the oxidation of pyrite, causing a pronounced acidification of the soil. However, becauseThiobacillus ferrooxidans functions optimally at pH values bellow 4.0, its activity cannot explain the initial pH drop from approximately neutral to about 4. This was shown to be a non-biological process, in which bacteria play an insignificant part. AlthoughThiobacillus thioparus andThiobacillus thiooxidans were isolated from the acidifying soil, they did not stimulate oxidation of FeS₂, but utilized reduced sulphur compounds, which are formed during the non-biological oxidation of FeS₂.Ethylene-oxide-sterilized and dry-sterilized soil inoculated with pure cultures of mixtures of various thiobacilli or with freshly sampled acid sulphate soil soil did not acidify faster than sterile blanks.Thiobacillus thiooxians. Thiobacillus thioparus. Thiobacillus intermedius andThiobacillus perometabolis increased from about 10⁴ to 10⁵ cells/ml in media with FeS₂ as energy source. However, FeS₂ oxidation in the inoculated media was not faster than in sterile blanks.Attempts to isolate microorganisms other thanThiobacillus ferrooxidans, like metallogenium orLeptospirillum ferrooxidans, which might also be involved in the oxidation of FeS₂ were not successful.Addition of CaCO₃ to the soil prevented acidification but did not stop non-biological oxidation of FeS₂.     

Numbers,diversity, and morphological characteristics of aerobic,chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina

The aerobic, chemoheterotrophic bacteria indigenous to deep aquifers and other subsurface sediments (depths to 265 m) at a site in South Carolina were characterized by direct microscopy, enumeration of viable cells, analysis of colony morphologies on plates, and analysis of cell morphologies of isolated strains. Substantial numbers of viable bacteria (10^5‐10⁸/g) were present in all transmissive, aquifer sediments, and their numbers did not decrease with depth. Fewer bacteria (<10³/g) were detected in nontransmissive, confining layers. The highest viable counts were obtained on dilute media, but 10–50% of the bacteria in most aquifer sediments also grew rapidly on concentrated, nutrient‐rich media (indicating a high degree of metabolic flexibility). Most of the bacteria were mesophilic; relatively few psychrophiles or thermophiles were detected (<10³/g; in many cases, none). The bacterial flora was diverse (11–62 distinct colony types on enumeration plates of most aquifer sediments). Diversity did not decrease with depth, but the composition of the microflora (based on colony analysis) varied extensively from one geological formation to another. Almost 95% of the platable colonies that grew on enumeration plates contained nonstreptomycete bacteria, more than 80% of which were gram‐negative rods. Light microscopy of films released from aquifer sediments by flotation revealed the presence of dividing cells and microcolonies, thus implying that the in situ deep aquifer microflora was more metabolically active than that seen previously in shallow aquifers.     

Biological control of streptococcal infection in Nile tilapia Oreochromis niloticus (Linnaeus, 1758) using filter‐feeding bivalve mussel Pilsbryoconcha exilis (Lea, 1838)

Since bivalve mussels are able to graze heavily on bacteria, in this paper it is hypothesized that when mussels are cultured with fish, the filtering efficiency of the mussels will keep the bacterial population below a certain threshold and thus assist in reducing the risk of bacterial disease outbreaks. The ability of the filter‐feeding bivalve mussel Pilsbryoconcha exilis to control Streptococcus agalactiae was tested in a laboratory‐scale tilapia culture system. Juvenile Nile tilapia (Oreochromis niloticus), the bivalve mussel as well as the bacteria were cultured at different combinations using four treatments: treatment‐1: mussel and bacteria but no fish, treatment‐2: tilapia and mussel but no bacteria, treatment‐3: tilapia and bacteria but no mussel, and treatment‐4: tilapia, mussels, and bacteria. All treatments were run in three replicates; stocking rates were 10 tilapia juveniles; five mussels; and about 3.5 × 10⁵ colony forming units (CFU) ml^?1 of bacteria in 50‐L aquaria with 40‐L volume. The mussel reduced the bacterial population by 83.6–87.1% in a 3‐week period whereas in the absence of the mussel, the bacterial counts increased by 31.5%. Oresence of the mussel also resulted in significantly higher growth and lower mortality of tilapia juveniles than when the mussel was absent. The results of this experiment suggest that the freshwater mussel P. exilis could control the population of S. agalactiae in a laboratory‐scale tilapia culture system. Future studies should focus on the dynamic interactions among fish, mussels, and bacteria as well as on how input such as feed and other organic materials affect these interactions.     

Microbiological changes in whiting (Merlangius merlangus Linneaus, 1758) fillets during short‐term cold storage and a traditional ‘pastrami‐like’ treatment

The objective of this study was to test the effects of salt‐dried whiting (Merlangius merlangus) fillet storage when treated with a special paste and stored covered. For this purpose whiting fillets were salt‐dried at 4–6°C for 15 days. A subsequent test series involved a paste mixture prepared from ground fenugreek, cumin seeds, black pepper, red pepper powder and garlic. The fillets were coated with this paste and air‐dried (15–20°C) for 5 days. All microbiological changes during this drying period were noted. The aerobic mesophilic bacterial counts decreased significantly (P < 0.05) from 5.08 ± 0.20 log cfu g^?1 to 3.24 ± 0.06 log cfu g^?1 after 15 days of salt‐drying. After then covering with paste and drying for 5 days (at 15–20°C), the aerobic mesophilic and lactic acid bacteria counts of the fillets increased to 6.05 ± 0.45 and 5.85 ± 0.06 log cfu g^?1, respectively. The pH values of dried whiting fillets changed after 15 days of dry salting (from 6.1 to 6.4), but after coating and drying with the paste, the pH values were 5.6 on day 5. Enterobactericeae were few in number at the start of salt‐drying (about 1.20 ± 0.15 log cfu g^?1), but their number decreased to <1.0 log cfu g^?1 after 15 days of dry‐salt storage. Staphylococcus aureus, Escherichia coli, mould and yeast were not detected at any time of drying. According to the resuts of the microbiological analyses, dried whiting fillet are considered safe for human consumption.     

Bacterial and Heterotrophic Nanoflagellate Densities and C‐biomass Estimates Along an Alaskan Tundra Transect with Prediction of Respiratory CO2 Efflux

Although tundra terrestrial ecology is significantly affected by global warming, we know relatively little about how eukaryotic microbial communities respond and how much microbial respiratory CO₂ may be released due to available organic nutrient sources in the permafrost melt. Prior research has shown a strong positive correlation between bacteria and fungi in some Arctic locales; this research focused on the relationships of terrestrial bacteria and heterotrophic nanoflagellates. The densities and estimated C‐biomass of bacteria and heterotrophic nanoflagellates (a major occurring group of protozoa) were assessed in 14 samples obtained along a 10 km transect in northwest AK during the summer of 2012. Two samples were taken, one at the top and one near the base of seven hummocks along the transect. Densities (no./g soil) of bacteria varied from 2.7–16 × 10⁹, and nanoflagellates 0.7–7.9 × 10⁷. C‐biomass (μg/g soil) of bacteria varied from 358 to 2,114, and nanoflagellates 12–37. Additionally, the rate of respiration was analyzed in the laboratory for each soil sample. A linear relationship between soil respiration and bacterial densities was obtained (20 °C): R_s = 12.32 + 14.07 B_d (p ? 0.01); where R_s is soil respiration (nmol/min/g soil) and B_d = bacterial density (no. × 10⁹/g soil).     

Biogeochemical probing of microbial communities in a basalt‐hosted hot spring at Kverkfjöll volcano,Iceland

We investigated bacterial and archaeal communities along an ice‐fed surficial hot spring at Kverkfjöll volcano—a partially ice‐covered basaltic volcano at Vatnajökull glacier, Iceland, using biomolecular (16S rRNA, apsA, mcrA, amoA, nifH genes) and stable isotope techniques. The hot spring environment is characterized by high temperatures and low dissolved oxygen concentrations at the source (68°C and <1 mg/L (±0.1%)) changing to lower temperatures and higher dissolved oxygen downstream (34.7°C and 5.9 mg/L), with sulfate the dominant anion (225 mg/L at the source). Sediments are comprised of detrital basalt, low‐temperature alteration phases and pyrite, with <0.4 wt. % total organic carbon (TOC). 16S rRNA gene profiles reveal that organisms affiliated with Hydrogenobaculum (54%–87% bacterial population) and Thermoproteales (35%–63% archaeal population) dominate the micro‐oxic hot spring source, while sulfur‐oxidizing archaea (Sulfolobales, 57%–82%), and putative sulfur‐oxidizing and heterotrophic bacterial groups dominate oxic downstream environments. The δ¹³C_org (‰ V‐PDB) values for sediment TOC and microbial biomass range from ?9.4‰ at the spring's source decreasing to ?12.6‰ downstream. A reverse effect isotope fractionation of ~3‰ between sediment sulfide (δ³⁴S ~0‰) and dissolved water sulfate (δ³⁴S +3.2‰), and δ¹⁸O values of ~ ?5.3‰ suggest pyrite forms abiogenically from volcanic sulfide, followed by abiogenic and microbial oxidation. These environments represent an unexplored surficial geothermal environment analogous to transient volcanogenic habitats during putative “snowball Earth” scenarios and volcano–ice geothermal environments on Mars.     

Bacterial formation of phosphatic laminites off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01′ S and 10°24′ S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS₂) and sphalerite (ZnS). Low δ³⁴S_pyrite values (average ?28.8‰) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide‐oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate‐reducing bacteria and associated sulfide‐oxidizing bacteria. Following an extraction–phosphorite dissolution–extraction procedure, molecular fossils of sulfate‐reducing bacteria (mono‐O‐alkyl glycerol ethers, di‐O‐alkyl glycerol ethers, as well as the short‐chain branched fatty acids i/ai‐C_15:0, i/ai‐C_17:0 and 10MeC_16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate‐reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate‐reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate‐reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate‐reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.     

Impact of acetaldehyde- and pyruvic acid-bound sulphur dioxide on wine lactic acid bacteria

Aims: To investigate the impact of acetaldehyde‐ and pyruvic acid‐bound sulphur dioxide on wine lactic acid bacteria (LAB). Methods and Results: Growth studies were performed where Oenococcus oeni, Pediococcus parvulus, Ped. damnosus and Lactobacillus hilgardii were inoculated into media containing various concentrations of acetaldehyde or pyruvic acid and an equimolar concentration of SO₂ at pH 3·50 and 3·70. Low concentrations of acetaldehyde‐ and pyruvic acid‐bound SO₂ were inhibitory to the growth of all bacteria although acetaldehyde‐bound SO₂ was generally more inhibitory than pyruvic acid‐bound SO₂. Inhibition was greater at pH 3·50 than 3·70, and Lact. hilgardii was the most sensitive to acetaldehyde‐bound SO₂, while O. oeni was the most sensitive to pyruvic acid‐bound SO₂. Degradation of SO₂‐bound acetaldehyde was observed for all LAB, and aside from O. oeni, there was also complete degradation of SO₂‐bound pyruvic acid at both pH values. O. oeni only degraded pyruvic acid at pH 3·70. Degradation of SO₂‐bound acetaldehyde or pyruvic acid did not correlate with bacterial growth as inhibition was always observed in media containing bound SO₂. Conclusions: Acetaldehyde‐ and pyruvic acid‐bound SO₂ were inhibitory to wine LAB growth at concentrations as low as 5 mg l^?1. Despite this inhibition, all wine LAB degraded SO₂‐bound acetaldehyde and pyruvic acid suggesting that bound SO₂ may have a bacteriostatic rather than bacteriocidal action. Significance and Impact of the Study: Sulphur dioxide bound to acetaldehyde or pyruvic acid is inhibitory to growth of wine LAB and must be considered when conducting the malolactic fermentation or controlling the growth of spoilage bacteria such as Pediococcus and Lactobacillus.     

Enthalpies and Entropies of Cd and Zn Adsorption onto Bacillus licheniformis and Enthalpies and Entropies of Zn Adsorption onto Bacillus subtilis from Isothermal Titration Calorimetry and Surface Complexation Modeling

Determining the thermodynamic driving force of metal-bacteria surface complexation is important for understanding why, from a thermodynamic perspective, these spontaneous reactions occur. We therefore determined the Gibbs energies, enthalpies, and entropies of Cd and Zn complexation onto Bacillus licheniformis and of Zn complexation onto Bacillus subtilis using surface complexation modeling and isothermal titration calorimetry. Our results indicated that Cd and Zn complexation onto Bacillus licheniformis is entropically driven at low pH and enthalpically driven at circumneutral pH. Zn complexation onto Bacillus subtilis is entropically driven, which suggests that Bacillus licheniformis has different donor ligands dominating reactivity around circumneutral pH.     

Helicobacter pylori does not mediate the formation of carcinogenic N-nitrosamines

Background. Both N‐nitroso compounds and colonization with Helicobacter pylori represent known risk‐factors for the development of gastric cancer. Endogenous formation of N‐nitroso compounds is thought to occur predominantly in acidic environments such as the stomach. At neutral pH, bacteria can catalyze the formation of N‐nitroso compounds. Based on experiments with a noncarcinogenic N‐nitroso compound as end product, and using only a single H. pylori strain, it was recently reported that H. pylori only displays a low nitrosation capacity. As H. pylori is a highly diverse bacterial species, it is reasonable to question the generality of this finding. In this study, several genetically distinct H. pylori strains are tested for their capacity to form carcinogenic N‐nitrosamines. Materials and Methods. Bacteria were grown in the presence of 0–1000 µM morpholine and nitrite (in a 1 : 1 molar ratio), at pH 7, 5 and 3. Results. Incubation of Neisseria cinerea (positive control) with 500 µM morpholine and 500 µM nitrite, resulted in a significant increase in formation of N‐nitrosomorpholine, but there was no significant induction of N‐nitrosomorpholine formation by any of the H. pylori strains, at any of the three pH conditions. Conclusion. H. pylori does not induce formation of the carcinogenic N‐nitrosomorpholine in vitro. The previously reported weak nitrosation capacity of H. pylori is not sufficient to nitrosate the more difficultly nitrosatable morpholine. This probably also holds true for other secondary amines. These results imply that the increased incidence of gastric cancer formation that is associated with gastric colonization by H. pylori is unlikely to result from the direct induced formation of carcinogenic nitrosamines by H. pylori. However, this has to be further confirmed in in vivo studies.     

Oral administration of Bifidobacterium longum prevents gut-derived Pseudomonas aeruginosa sepsis in mice

Aims: The aim of the study was to evaluate the efficacy of probiotics on gut‐derived sepsis caused by Pseudomonas aeruginosa in immunocompromised mice. Methods and Results: After oral inoculation of P. aeruginosa, mice were treated with cyclophosphamide to induce leucopenia and translocation of the intestinal P. aeruginosa into blood, thereby producing gut‐derived sepsis. In this model, administration of 1 × 10⁹ CFU of Bifidobacterium longum strain BB536 for 10 days significantly (P < 0·01) increased the survival rate compared with groups of mice administered either with Bifidobacterium breve strain ATCC 15700 or excipients contained in the probiotic bacterial powder. Administration of B. longum significantly decreased viable counts of P. aeruginosa in the liver and blood compared with other groups. Culture of intestinal contents revealed a significantly lower viable count of P. aeruginosa in the jejunum of B. longum‐treated mice compared with other groups of mice. Furthermore, in vitro data demonstrated that B. longum possessed apparently higher adherent activity to Caco‐2 cell monolayers and significantly suppressed the adherence of P. aeruginosa to the monolayers of cells compared with other groups. Conclusion: Oral administration of B. longum protects mice against gut‐derived sepsis caused by P. aeruginosa, and the effect may be due to interference of P. aeruginosa adherence to intestinal epithelial cells. Significance and Impact of this Study: This study demonstrated that oral administration of B. longum BB536 is effective to protect against opportunistic infection with drug‐resistant bacteria such as P. aeruginosa. The results suggest that probiotics may play an important role even in the immunocompromised patients.     

Effects of acidification on the breeding ecology of a stream‐dependent songbird,the Louisiana waterthrush (Seiurus motacilla)

1. We compared breeding ecology of the Louisiana waterthrush (Seiurus motacilla) on acidified and circumneutral streams in the Appalachian Highlands of Southwestern Pennsylvania from 1996 to 2005. 2. Headwater streams impacted by acid mine drainage and/or acidic precipitation showed reduced pH (range 4.5–5.5) compared to four circumneutral streams (pH c. 7). Acid‐sensitive taxa, including most mayflies (Ephemeroptera), were almost completely absent from acidified streams, whereas several acid‐tolerant taxa, especially stonefly (Plecoptera) genera Leuctra and Amphinemura, were abundant. 3. Louisiana waterthrush breeding density (c. 1 territory km^?1) was significantly reduced on acidified streams compared to circumneutral streams (>2 territories km^?1). Territories on acidified streams were almost twice as long as on circumneutral streams. Territories usually were contiguous on circumneutral streams, but they were often disjunct on acidified streams. Breeding density declined on one acidified stream that we studied over a 10‐year period. 4. Clutch initiation was significantly delayed on acidified streams, on average by 9 days in comparison to circumneutral streams, and first‐egg dates were inversely related to breeding density. Birds nesting along acidified streams laid smaller clutches, and nestlings had shorter age‐adjusted wing lengths. Stream acidity had no effect on nest success or annual fecundity (fledglings/female). However, the number of young fledged km^?1 was nearly twice as high on circumneutral streams as on acidified streams. 5. Acidified streams were characterized by a younger, less site‐faithful breeding population. Individuals were less likely to return multiple years to breed, allowing inexperienced breeders to settle on acidified streams. Pairing success was lower on acidified streams, and we observed four cases of waterthrushes emigrating from territories on acidified streams to nearby circumneutral streams in the following year. 6. We conclude that acidified headwaters constitute lower quality habitat for breeding Louisiana waterthrush. However, breeding birds can apparently compensate for reduced prey resources to fledge young on acidified streams by increasing territory size, foraging in peripheral non‐acidified areas, and by provisioning young with novel prey.     

A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp.bulgaricus and Streptococcus thermophilus

Aims: We have developed a direct viable count (DVC)‐FISH procedure for quickly and easily discriminating between viable and nonviable cells of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains, the traditional yogurt bacteria. Methods and Results: direct viable count method has been modified and adapted for Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus analysis by testing different times of incubation and concentrations of DNA‐gyrase inhibitors. DVC procedure has been combined with fluorescent in situ hybridization (FISH) for the specific detection of viable cells of both bacteria with specific rRNA oligonucleotide probes (DVC‐FISH). Of the four antibiotics tested (novobiocin, nalidixic acid, pipemidic acid and ciprofloxacin), novobiocin was the most effective for DVC method and the optimum incubation time was 7 h for both bacteria. The number of viable cells was obtained by the enumeration of specific hybridized cells that were elongated at least twice their original length for Lactobacillus and twice their original size for Streptococcus. Conclusions: This technique was successfully applied to detect viable cells in inoculated faeces. Significance and Impact of the Study: Results showed that this DVC‐FISH procedure is a quick and culture‐independent useful method to specifically detect viable Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus in different samples, being applied for the first time to lactic acid bacteria.     

Virus dynamics in a large epishelf lake (Beaver Lake,Antarctica)

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Sulphur cycling in a Neoarchaean microbial mat

Multiple sulphur (S) isotope ratios are powerful proxies to understand the complexity of S biogeochemical cycling through Deep Time. The disappearance of a sulphur mass‐independent fractionation (S‐MIF) signal in rocks <~2.4 Ga has been used to date a dramatic rise in atmospheric oxygen levels. However, intricacies of the S‐cycle before the Great Oxidation Event remain poorly understood. For example, the isotope composition of coeval atmospherically derived sulphur species is still debated. Furthermore, variation in Archaean pyrite δ³⁴S values has been widely attributed to microbial sulphate reduction (MSR). While petrographic evidence for Archaean early‐diagenetic pyrite formation is common, textural evidence for the presence and distribution of MSR remains enigmatic. We combined detailed petrographic and in situ, high‐resolution multiple S‐isotope studies (δ³⁴S and Δ³³S) using secondary ion mass spectrometry (SIMS) to document the S‐isotope signatures of exceptionally well‐preserved, pyritised microbialites in shales from the ~2.65‐Ga Lokammona Formation, Ghaap Group, South Africa. The presence of MSR in this Neoarchaean microbial mat is supported by typical biogenic textures including wavy crinkled laminae, and early‐diagenetic pyrite containing <26‰ μm‐scale variations in δ³⁴S and Δ³³S = ?0.21 ± 0.65‰ (±1σ). These large variations in δ³⁴S values suggest Rayleigh distillation of a limited sulphate pool during high rates of MSR. Furthermore, we identified a second, morphologically distinct pyrite phase that precipitated after lithification, with δ³⁴S = 8.36 ± 1.16‰ and Δ³³S = 5.54 ± 1.53‰ (±1σ). We propose that the S‐MIF signature of this secondary pyrite does not reflect contemporaneous atmospheric processes at the time of deposition; instead, it formed by the influx of later‐stage sulphur‐bearing fluids containing an inherited atmospheric S‐MIF signal and/or from magnetic isotope effects during thermochemical sulphate reduction. These insights highlight the complementary nature of petrography and SIMS studies to resolve multigenerational pyrite formation pathways in the geological record.     

Distribution of aerobic bacteria,protozoa, algae,and fungi in deep subsurface sediments

The distribution of microorganisms in deep subsurface profiles was determined at three sites at the Savannah River Plant, Aiken, South Carolina. Acridine orange direct counts (AODC) of bacteria were highest in surface soil samples and declined to the 10⁶ to 10⁷ per gram range in the subsurface, but then did not decline further with depth. In the subsurface, AODC values varied from layer to layer, the highest being found in samples from sandy aquifer formations and the lowest in clayey interbed layers. Sandy aquifer sediments also contained the highest numbers of viable bacteria as determined by aerobic spread plate counts (CFU) on a dilute heterotrophic medium. In some of these samples bacterial CFU values approached 100% of the AODC values. Viable protozoa (amoebae and flagellates, but no ciliates) were found in samples with high bacterial CFU values. A variety of green algae, phytoflagellates, diatoms, and a few cyanobacteria were found at low population densities in samples from two of the three boreholes. Low numbers of fungi were evenly distributed throughout the profiles at all three sites. Microbial population density estimates correlated positively with sand content and pore‐water pH, and negatively with clay content and pore‐water metal concentration. A large diversity of prokaryotic and eukaryotic microorganisms was found in samples with high population densities. A survey of bacterial strains isolated from subsurface samples revealed associations of gram‐positive bacteria with high clay sediments and gram‐negative bacteria with sandy sediments. The ability to deposit lipophilic storage material (presumably poly‐ß‐hydroxybutyrate) was found in a high proportion of isolates from sandy sediments, but only rarely in isolates from high clay sediments.     

Detection of viable Escherichia coli O157:H7 by ethidium monoazide real-time PCR

Aims: The aim of this study was to develop and optimize a novel method that combines ethidium bromide monoazide (EMA) staining with real‐time PCR for the detection of viable Escherichia  coli O157:H7 in ground beef. EMA can penetrate dead cells and bind to intracellular DNA, preventing its amplification via PCR. Methods and Results: Samples were stained with EMA for 5 min, iced for 1 min and exposed to bright visible light for 10 min prior to DNA extraction, to allow EMA binding of the DNA from dead cells. DNA was then extracted and amplified by TaqMan^® real‐time PCR to detect only viable E. coli O157:H7 cells. The primers and TaqMan^® probe used in this study target the uidA gene in E. coli O157:H7. An internal amplification control (IAC), consisting of 0·25 pg of plasmid pUC19, was added in each reaction to prevent the occurrence of false‐negative results. Results showed a reproducible application of this technique to detect viable cells in both broth culture and ground beef. EMA, at a final concentration of 10 μg ml^?1, was demonstrated to effectively bind DNA from 10⁸ CFU ml^?1 dead cells, and the optimized method could detect as low as 10⁴ CFU g^?1 of viable E. coli O157:H7 cells in ground beef without interference from 10⁸ CFU g^?1 of dead cells. Conclusions: EMA real‐time PCR with IAC can effectively separate dead cells from viable E. coli O157:H7 and prevent amplification of DNA in the dead cells. Significance and Impact of the Study: The EMA real‐time PCR has the potential to be a highly sensitive quantitative detection technique to assess the contamination of viable E. coli O157:H7 in ground beef and other meat or food products.     

Evaluation of Bacterial Community Structure and Its Influence on Sulfide Oxidation in a Bio-Leaching Environment

The mechanism of sulfide oxidation by adhering bacteria (direct oxidation mechanism) and by ferric ion in the aqueous phase was studied by quantitative assessment of bacterial activity on the sulfide surface. To probe for the principal bacterial species on the surface and in the supernatant, a library of DNA genes encoding portions of bacterial 16S rRNA was constructed. The PCR-amplified DNA from the bacterial populations was cloned employing PROMEGA's pGEM-T Easy Vector system. The clone frequency indicated that iron-oxidizing bacteria were dominant in the liquid phase, while Acidithiobacillus ferroixdans, which is both sulfur and iron oxidizer was the most prevalent on the sulfide surface. Samples of crystalline pyrite were exposed to the bacterial consortium to evaluate surface alterations caused by bacteria. Chemical (abiotic) oxidation experiments with ferric ion as the oxidant were carried out in parallel with the biological oxidation tests. Changes in the surface topography were monitored by atomic force microscopy (AFM) while changes in surface chemistry were examined by Raman spectroscopy. Bacterial attachment resulted in a 53% increase in the specific surface area in comparison to a 13% increase caused by chemical (ferric ion) oxidation. The oxidation rate was assessed by evaluating the iron release. After corrections for surface area changes, the specific abiotic (oxidation by Fe^{3 +}) and biotic oxidation rates with adhering bacteria were nearly the same (2.6 × 10^{? 9} mol O₂/s/m² versus 3.3 × 10^{? 9} mol O₂/s/m²) at pH = 2 and a temperature of 25°C. The equality of rates implies that the availability of ferric ion as the oxidant is rate limiting.