Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.

Understanding the geochemical cycling of sulfur in sediments is important because it can have implications for both modern environments (e.g., deterioration of water quality) and interpretation of the ancient past (e.g., sediment C/S ratios can be used as indicators of palaeodepositional environment). This study investigates the geochemical characteristics of sulfur, iron, and organic carbon in fluvial and coastal surface sediments of the Laizhou Bay region, China. A total of 63 sediment samples were taken across the whole Laizhou Bay marine region and the 14 major tidal rivers draining into it. Acid volatile sulfur, chromium (II)-reducible sulfur and elemental sulfur, total organic carbon, and total nitrogen were present in higher concentrations in the fluvial sediment than in the marine sediment of Laizhou Bay. The composition of reduced inorganic sulfur in surface sediments was dominated by acid volatile sulfur and chromium (II)-reducible sulfur. In fluvial sediments, sulfate reduction and formation of reduced inorganic sulfur were controlled by TOC and reactive iron synchronously. High C/S ratios in the marine sediments indicate that the diagenetic processes in Laizhou Bay have been affected by rapid deposition of sediment from the Yellow River in recent decades.

Background Monitoring of minimal residual disease (MRD) has become a frontline clinical practice in the treatment of virtually all childhood acute lymphoblastic leukemia (ALL) cases and in many cases of adult patients with ALL. The MRD diagnostics has proven to be the strongest prognostic factor allowing for risk group assignment into different treatment arms. The MRD techniques need to be sensitive (≤10–4), which means, the ability to detect one malignant cell among 10 000 normal cells; broadly applicable; accurate; reliable; fast; and affordable. Aim The objective of this study is to evaluate the analysis of immunoglobulin heavy chain (IGH) or T-cell receptor (TCR) gene rearrangements as targets for MRD assessment in ALL, allowing early detection of relapsed cases, compare with the results of morphological evaluation of the same cases and to risk stratify patients with ALL according to the MRD assessment as a prognostic marker independent and superior to other conventional risk factors. Patients and methods Overall, 30 patients (15 males and 15 females) with age ranged from 1 to 25 years old were included in this study. Patients were subjected to full medical history, clinical examination, laboratory examinations such as complete blood count, bone marrow aspirate smear examination, cytochemistry, and immunophenotyping. The molecular studies done by real-time PCR were performed using consensus primers and allele-specific primers for (IGH) or (TCR) gene rearrangements as targets to detect MRD. The ALL cases were assessed by real-time quantitative PCR at the time of diagnosis and at the end of induction chemotherapy, and comparative cycle threshold (Ct) relative quantification method was used for quantitative gene expression. Results The results showed discrepancy between the morphologic examination for ALL assessment depending on the 5% blast index as an indicator of remission or nonremission; morphological nonremissions (>5% blast) were detected in eight (26.7%) cases whereas 22 (73.3%) cases showed morphological remissions ( Conclusion Approximately 81% of ALL cases previously diagnosed as being in the remission state depending on the morphologic assessment only tend to harbor MRD as evident by positive MRD assessment using real-time PCR. The molecular assessment of MRD allows early detection of relapse with chance of intervention and tailoring of treatment according to the patients' need. It was found that there was no relation between MRD results and risk stratification in ALL according to age and white blood cell at diagnosis; this confirms that detection of MRD of leukemic cells can be considered a superior prognostic marker of relapse, independent from conventional prognostic factors. The risk classification in ALL based on MRD results could be used to guide the final treatment strategy and predict early relapse; this should allow prediction of response and relapse while patients are still in the state of clinical remission and morphological remission too.

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12-100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.

Froth treatment tailings (FTT) are a byproduct of bitumen extraction in Alberta’s oil sands and, while the smallest tailings stream by volume, they present disproportionate challenges for closure and reclamation. Produced during froth treatment, where diluent such as naphtha is added to separate bitumen from water and solids, FTT contain residual hydrocarbons and sulfide minerals like pyrite. These constituents can influence redox conditions, microbial activity, and hydrocarbon degradation processes, ultimately affecting long-term deposit behavior. Despite their importance, FTT remain understudied compared with other tailings types, especially in the context of terrestrial beach deposits targeted for reclamation.This study investigated the spatial and vertical distribution of hydrocarbons and microbial communities across a 1.4 km transect of a naphtha-based FTT beach deposit at Syncrude’s Mildred Lake Settling Basin. Samples were collected from six locations spanning the pond edge to a reclamation dyke, with depths ranging from 0.15 to 46 m. Chemical analysis revealed that petroleum hydrocarbon (PHC) and residual naphtha concentrations reflected deposition history, with higher concentrations found in deeper, older FTT near the dyke and at shallower depths adjacent to the pond. Naphtha concentrations were most strongly correlated with heavier PHC fractions (F2–F4), while toluene and ethylbenzene emerged as key indicators of microbial variation.Distinct microbial communities were observed in FTT relative to the underlying coarse tailings, with reduced diversity at depths greater than ~30 m. FTT were enriched in hydrocarbon degraders (e.g., Pseudomonas), sulfur-cycling taxa (Thiobacillus, Desulfovibrio, Desulfotomaculales), and methanogens (Methanosaeta). Community composition varied with depth, distance from the pond, and presence of FTT, with the strongest drivers being PHC concentrations and pyrite content. These findings suggest that residual hydrocarbons act both as substrates and stressors, shaping microbial ecology while interacting with geochemical processes such as sulfur reduction and oxidation as well as methanogenesis.Together, this work provides one of the first spatially resolved assessments of FTT deposits illustrating how residual diluent, hydrocarbons, and microbial processes interact to influence subsurface conditions. Accurate characterization of FTT is essential for predicting long-term behavior, guiding the design of closure landforms, and informing reclamation monitoring programs.

Anaerobic degradation of organic material generally proceeds through a sequence of steps, including polymer hydrolysis, fermentation and respiration or methanogenesis. The intermediates, such as volatile fatty acids (VFA) or H(2), are generally maintained at low concentration, showing a close coupling of the terminal oxidation to fermentation. We exposed marine sediments to extreme temperature perturbations to study the nature and robustness of this coupling. Bacterial sulfate reduction and its dependence on fermentation were studied experimentally over a broad temperature range of -0.3 to 40 degrees C in sediments from temperate and permanently cold environments. In an Arctic sediment from Svalbard, the apparent optimum temperature for sulfate reduction decreased with prolonged incubation, whereas sulfate reduction rates increased. In a temperate sediment from the North Sea, the apparent optimum temperature was higher and did not change with incubation time. Up to a critical temperature, the concentrations of VFA remained low, <3 microM for acetate and <1 microM for the other VFA, the H(2) concentration showed thermodynamic control by sulfate-reducing bacteria, revealing a close coupling of fermentation and sulfate reduction. Above the critical temperature, the concentrations of VFA and H(2) increased transiently by 100-1000-fold. According to the different in situ temperatures of the samples, the critical temperature was lower for sediments from the Arctic than from the North Sea. The H(2) concentrations decreased again upon prolonged incubation to values typical for sulfate-depleted methanogenic sediments. This suggests that fermentative bacteria and methanogenic archaea in both sediments tolerated higher temperatures than the sulfate-reducing community.

Differences in methylmercury (CH(3)Hg) production normalized to the sulfate reduction rate (SRR) in various species of sulfate-reducing bacteria (SRB) were quantified in pure cultures and in marine sediment slurries in order to determine if SRB strains which differ phylogenetically methylate mercury (Hg) at similar rates. Cultures representing five genera of the SRB (Desulfovibrio desulfuricans, Desulfobulbus propionicus, Desulfococcus multivorans, Desulfobacter sp. strain BG-8, and Desulfobacterium sp. strain BG-33) were grown in a strictly anoxic, minimal medium that received a dose of inorganic Hg 120 h after inoculation. The mercury methylation rates (MMR) normalized per cell were up to 3 orders of magnitude higher in pure cultures of members of SRB groups capable of acetate utilization (e.g., the family Desulfobacteriaceae) than in pure cultures of members of groups that are not able to use acetate (e.g., the family Desulfovibrionaceae). Little or no Hg methylation was observed in cultures of Desulfobacterium or Desulfovibrio strains in the absence of sulfate, indicating that Hg methylation was coupled to respiration in these strains. Mercury methylation, sulfate reduction, and the identities of sulfate-reducing bacteria in marine sediment slurries were also studied. Sulfate-reducing consortia were identified by using group-specific oligonucleotide probes that targeted the 16S rRNA molecule. Acetate-amended slurries, which were dominated by members of the Desulfobacterium and Desulfobacter groups, exhibited a pronounced ability to methylate Hg when the MMR were normalized to the SRR, while lactate-amended and control slurries had normalized MMR that were not statistically different. Collectively, the results of pure-culture and amended-sediment experiments suggest that members of the family Desulfobacteriaceae have a greater potential to methylate Hg than members of the family Desulfovibrionaceae have when the MMR are normalized to the SRR. Hg methylation potential may be related to genetic composition and/or carbon metabolism in the SRB. Furthermore, we found that in marine sediments that are rich in organic matter and dissolved sulfide rapid CH(3)Hg accumulation is coupled to rapid sulfate reduction. The observations described above have broad implications for understanding the control of CH(3)Hg formation and for developing remediation strategies for Hg-contaminated sediments.

A global model for the early diagenesis of organic carbon and organic phosphorus in marine sediments

Controls on volatile fatty acid concentrations in marine sediments (Baltic Sea)

SUMMARY: The sources of sulphide which appeared in the profundal zone of Blelham Tarn (English Lake District) were investigated. In experimental sediment cores, the absence of sulphate in the overlying water resulted in a drastic decrease in the release of sulphide, which suggested that sulphate reduction was a major contributor to the process. The quantity of suphide produced was much less than that of sulphate removed. This, and the inability to detect free sulphide in sediment interstitial water, was attributed to its rapid precipitation as FeS. In the absence of sulphate, production of sulphide would be from organic sources such as protein. Most probable number estimates indicated that the population of bacteria capable of producing sulphide from cysteine was much larger than that of sulphate reducers. Trace additions of 35S-labelled sulphate, cysteine and methionine were used to determine their turnover time to sulphide. Sulphate was turned over the fastest and methionine the slowest, and the turnover time was always shorter in profundal sediment. Poor recoveries of added label from littoral sediments were thought to be due to adsorption and higher rates of assimilation. Estimates of flux based on concentrations of sulphate and organic sulphur suggested that putrefaction was a more important source of sulphide in the littoral zone but contributed less than sulphate reduction in the profundal sediments.

Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle

This study investigated the effect of acetate and methanol as co-substrates on anaerobic biodegradation of total petroleum hydrocarbons (TPHs, C10-C40) in marine sediment. The findings evidenced that the degradation of TPH can be enhanced by adding acetate or methanol. The addition of acetate was generally more favorable than the addition of methanol for the TPH degradation. Both sulfate reduction and methanogenesis occurred in the acetate-treated sediment. However, the depletion of SO4 (2-) inhibited sulfate reduction over the incubation period. Only methanogenesis was prevalent in the methanol-treated sediment within the whole incubation period. The degradation of TPH fractions with higher carbon number ranges (C31-C40) was speculated to be more favored under sulfate-reducing condition, while TPH fractions with lower carbon number ranges (C10-C20) were preferentially degraded under methanogenic condition. The 16S rRNA clone library-based analysis revealed that the addition of different co-substrates led to distinct structures of the microbial community. Clones related to sulfate-reducing Desulfobacterales were the most abundant in the sediment dosed with acetate. Clones related to Clostridiales predominated in the sediment dosed with methanol. Acetoclastic methanogens were found to be the predominant archaeal species in the sediment dosed with acetate, while both acetoclastic methanogens and hydrogenotrophic methanogens accounted for large proportions in the sediment dosed with methanol. The results obtained in this study will contribute to more comprehensive knowledge on the role of acetate and methanol as co-substrates in biostimulation of petroleum-hydrocarbon-contaminated marine sediment.

Sulphur isotope geochemistry of pyrite from the Upper Cretaceous Marshybank Formation, Western Interior Basin

Recent localised sulphate reduction and pyrite formation in a fissured Chalk aquifer

The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.

Biological sulfate reduction can be used for the removal and recovery of oxidized sulfur compounds and metals from waste streams. However, the costs of conventional electron donors, like hydrogen and ethanol, limit the application possibilities. Methane from natural gas or biogas would be a more attractive electron donor. Sulfate reduction with methane as electron donor prevails in marine sediments. Recently, several authors succeeded in cultivating the responsible microorganisms in vitro. In addition, the process has been studied in bioreactors. These studies have opened up the possibility to use methane as electron donor for sulfate reduction in wastewater and gas treatment. However, the obtained growth rates of the responsible microorganisms are extremely low, which would be a major limitation for applications. Therefore, further research should focus on novel cultivation techniques. © The Author(s) 2010.