A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Sorption of radioiodide in an acidic, nutrient-poor boreal bog: insights into the microbial impact.

Batch sorption experiments were conducted to evaluate the sorption behaviour of iodide and the microbial impact on iodide sorption in the surface moss, subsurface peat, gyttja, and clay layers of a nutrient-poor boreal bog. The batch distribution coefficient (Kd) values of iodide decreased as a function of sampling depth. The highest Kd values, 4800 L/Kg dry weight (DW) (geometric mean), were observed in the fresh surface moss and the lowest in the bottom clay (geometric mean 90 mL/g DW). In the surface moss, peat and gyttja layers, which have a high organic matter content (on average 97%), maximum sorption was observed at a pH between ∼ 4 and 5 and in the clay layer at pH 2. The Kd values were significantly lower in sterilized samples, being 20-fold lower than the values found for the unsterilized samples. In addition, the recolonization of sterilized samples with a microbial population from the fresh samples restored the sorption capacity of surface moss, peat and gyttja samples, indicating that the decrease in the sorption was due to the destruction of microbes and supporting the hypothesis that microbes are necessary for the incorporation of iodide into the organic matter. Anoxic conditions reduced the sorption of iodide in fresh, untreated samples, similarly to the effect of sterilization, which supports the hypothesis that iodide is oxidized into I2/HIO before incorporation into the organic matter. Furthermore, the Kd values positively correlated with peroxidase activity in surface moss, subsurface peat and gyttja layers at +20 °C, and with the bacterial cell counts obtained from plate count agar at +4 °C. Our results demonstrate the importance of viable microbes for the sorption of iodide in the bog environment, having a high organic matter content and a low pH.

The microbial impact on the sorption behaviour of selenite in an acidic, nutrient-poor boreal bog.

(79)Se is among the most important long lived radionuclides in spent nuclear fuel and selenite, SeO3(2-), is its typical form in intermediate redox potential. The sorption behaviour of selenite and the bacterial impact on the selenite sorption in a 7-m-deep profile of a nutrient-poor boreal bog was studied using batch sorption experiments. The batch distribution coefficient (Kd) values of selenite decreased as a function of sampling depth and highest Kd values, 6600 L/kg dry weight (DW), were observed in the surface moss and the lowest in the bottom clay at 1700 L/kg DW. The overall maximum sorption was observed at pH between 3 and 4 and the Kd values were significantly higher in unsterilized compared to sterilized samples. The removal of selenite from solution by Pseudomonas sp., Burkholderia sp., Rhodococcus sp. and Paenibacillus sp. strains isolated from the bog was affected by incubation temperature and time. In addition, the incubation of sterilized surface moss, subsurface peat and gyttja samples with added bacteria effectively removed selenite from the solution and on average 65% of selenite was removed when Pseudomonas sp. or Burkholderia sp. strains were used. Our results demonstrate the important role of bacteria for the removal of selenite from the solution phase in the bog environment, having a high organic matter content and a low pH.

Factors affecting the sorption of cesium in a nutrient-poor boreal bog.

(135)Cs is among the most important radionuclides in the long-term safety assessments of spent nuclear fuel, due to its long half-life of 2.3 My and large inventory in spent nuclear fuel. Batch sorption experiments were conducted to evaluate the sorption behavior of radiocesium ((134)Cs) in the surface moss, peat, gyttja, and clay layers of 7-m-deep profiles taken from a nutrient-poor boreal bog. The batch distribution coefficient (Kd) values of radiocesium increased as a function of sampling depth. The highest Kd values, with a geometric mean of 3200 L/kg dry weight (DW), were observed in the bottom clay layer and the lowest in the 0.5-1.0 m peat layer (50 L/kg DW). The maximum sorption in all studied layers was observed at a pH between 7 and 9.5. The in situ Kd values of (133)Cs in surface Sphagnum moss, peat and gyttja samples were one order of magnitude higher than the Kd values obtained using the batch method. The highest in situ Kd values (9040 L/kg DW) were recorded for the surface moss layer. The sterilization of fresh surface moss, peat, gyttja and clay samples decreased the sorption of radiocesium by 38%, although the difference was not statistically significant. However, bacteria belonging to the genera Pseudomonas, Paenibacillus, Rhodococcus and Burkholderia isolated from the bog were found to remove radiocesium from the solution under laboratory conditions. The highest biosorption was observed for Paenibacillus sp. V0-1-LW and Pseudomonas sp. PS-0-L isolates. When isolated bacteria were added to sterilized bog samples, the removal of radiocesium from the solution increased by an average of 50% compared to the removal recorded for pure sterilized peat. Our results demonstrate that the sorption of radiocesium in the bog environment is dependent on pH and the type of the bog layer and that common environmental bacteria prevailing in the bog can remove cesium from the solution phase.

Generation of in vitro natural cytotoxicity of horse lymphocytes against sarcoid-derived tumor cells not expressing major histocompatibility complex antigens.

OBJECTIVE: To analyze in vitro lymphocyte-mediated immune responses of horses with sarcoids against allogeneic sarcoid cells containing endogenous retrovirus but not expressing major histocompatibility complex antigens. DESIGN: Lymphocyte-mediated immune reactions were assessed by means of proliferative responses in mixed lymphocyte tumor cell culture (MLTC) assay and lymphocyte-mediated cytotoxicity against various equine target cells. ANIMALS: 12 horses with sarcoid tumors and 15 control horses. PROCEDURE: Blood lymphocytes were cocultured in MLTC with allogeneic sarcoid cells (Mc-1, BayMc-1), equine testis cells, or normal equine dermal fibroblasts. Lymphocytes were assayed for proliferative responses by [3H]thymidine uptake and for cytotoxicity against the same targets by 51Cr release assay. The lymphocyte populations were analyzed for some common surface markers. RESULTS: Lymphocytes from horses with sarcoids exerted an anamnestic proliferative response in MLTC against Mc-1 cells, but this procedure never generated cytotoxic lymphocytes. However, lymphocytes from all horses cultured in medium with 10% allogeneic serum only had selective. natural cytotoxicity against Mc-1 that was generated without DNA synthesis. Approximately 80% of the lymphocytes disappeared during culture; however the remaining population of small, viable lymphocytes indicated a decrease of CD4+ T lymphocytes, but numbers of T cells with receptors for Helix pomatia A hemagglutinin were unaffected. Few lymphocytes had Fc-receptors for IgG, were complement-reactive positive cells or were B cells expressing surface immunoglobulin. CONCLUSIONS: Results may indicate a natural defense system, which preferentially recognizes and lyses tumor cells that are deficient in surface expression of major histocompatibility complex antigens, without intervention of conventional T-cell receptors or antibodies.