Microbial growth and resuscitation alter community structure after perturbation

Influence of the Use of an Additional Oxidant (Chlorine Dioxide) in Water Treatment on Swimming Pool Water Quality

This article presents the results of experiments on the effect of chlorine dioxide, applied as an additional oxidant, on swimming pool water quality. Three doses of chlorine dioxide were applied: 22, 44 and 66 mg/m3. At each research stage, prior to the actual experiment, in which the oxidant was dosed, the background was tested, i.e., water samples were taken from a conventional treatment system (without chlorine dioxide). The experiments showed that chlorine dioxide effectively removes organic compounds and their chlorine derivatives. For the highest dose of ClO2, CODMn decreased by almost 88% and chloroform concentration by 75%. Chlorine dioxide also effectively supports water disinfection. At the highest dose, the number of mesophilic bacteria decreased by 60% and the number of psychrophiles by 94%. However, after the dosing of this oxidant had been discontinued, a deterioration of the microbiological water quality and the secondary growth of microorganisms were observed. Chlorine dioxide also caused an increase in conductivity and the concentration of inorganic compounds (nitrates, total chlorates and chlorites). The effect of this agent on the combined chlorine concentration was not observed. The reported experiments have shown that this measure is not unequivocally beneficial in terms of improving swimming pool water quality.

Microbial lipid biomarkers detected in deep subsurface black shales

Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations. Here, we describe the distribution of bacterial ester-linked phospholipid fatty acids (PLFA) and diglyceride fatty acids (DGFA) in sidewall cores retrieved from three distinct geologic horizons collected to 2275 m below ground surface in a Marcellus Shale well, West Virginia, USA. We examined the abundance and variety of PLFA and DGFA prior to energy development within and above the Marcellus Shale Formation into the overlying Mahantango Formation of the Appalachian Basin. Lipid biomarkers in the cores suggest the presence of microbial communities comprising Gram (+), Gram (-) as well as stress indicative biomarkers. Microbial PLFA and DGFA degradation in the subsurface can be influenced by stressful environmental conditions associated with the subsurface. The PLFA concentration and variety were higher in the transition zone between the extremely low permeability Marcellus Shale Formation and the more permeable Mahantango Formation. In contrast to this distribution, more abundant and diverse DGFA membrane profiles were associated with the Mahantango Formation. The stress indicative biomarkers like the trans-membrane fatty acids, oxiranes, keto-, and dimethyl lipid fatty acids were present in all cores, potentially indicating that the bacterial communities had experienced physiological stress or nutrient deprivation during or after deposition. The DGFA profiles expressed more stress indicative biomarkers as opposed to the PLFA membrane profiles. These findings suggest the probable presence of indigenous microbial communities in the deep subsurface shale and also improves our understanding of microbial survival mechanisms in ancient deep subsurface environments.

Effects of biosolids from a wastewater treatment plant receiving manufactured nanomaterials on Medicago truncatula and associated soil microbial communities at low nanomaterial concentrations

Concern has grown regarding engineered nanomaterials (ENMs) entering agricultural soils through the application of biosolids and their possible effects on agroecosystems, even though the ENMs are extensively transformed. The effects of exposure to biosolids containing transformation products of these ENMs at low concentrations remain largely unexplored. We examined the responses of Medicago truncatula and its symbiotic rhizobia Sinorhizobium meliloti exposed to soil amended with biosolids from WWTP containing low added concentrations of ENMs (ENM Low), bulk/dissolved metals (bulk/dissolved Low), or no metal additions (control). We targeted adding approximately 5mg/kg of Ag and 50mg/kg of Zn, and Ti. Measured endpoints included M. truncatula growth, nodulation, changes in the expression of stress response genes, uptake of metals (Ag, Zn and Ti) into shoots, and quantification of S. meliloti populations and soil microbial communities. After 30days exposure, no effects on root or shoot biomass were observed in ENM Low and bulk/dissolved Low treatments, whereas both treatments had a larger average number of nodules (5.7 and 5.57, respectively) compared to controls (0.33). There were no significant differences in either total accumulated metal or metal concentrations in shoots among the treatments. Expression of five stress-related genes (metal tolerance protein (MTP), metal transporter (MTR), peroxidase (PEROX), NADPH oxidase (NADPH) and 1-aminocyclopropane-1-carboxylate oxidase-like protein (ACC_Oxidase)) was significantly down-regulated in both bulk/dissolved Low and ENM Low treatments. However, a change in soil microbial community composition and a significant increase in total microbial biomass were observed in ENM Low relative to control. The ENM Low treatment had increased abundance of Gram-negative and anaerobic bacteria and reduced abundance of eukaryotes compared to control. The study demonstrated that although there were some subtle shifts in microbial community composition, plant health was minimally impacted by ENMs within the time frame and at the low exposure concentrations used in this study.

Modified Lipid Extraction Methods for Deep Subsurface Shale

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery.

Biodegradation in contaminated aquifers: incorporating microbial/molecular methods

In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.

Effects of soil storage on the microbial community and degradation of metsulfuron-methyl

The effect storage had on the microbial biomass in two soils (Trevino and Fargo) was compared to the effect storage had on each soil's capacity to degrade metsulfuron-methyl. Soils were collected from the field and used fresh (<3 weeks old) or stored at 20 and 4 degrees C for 3 or 6 months. The phospholipid fatty acid content of the soils was used to monitor changes in the microbial biomass during storage and incubation in a flow-through apparatus. In both soils, [phenyl-U-14C]metsulfuron-methyl was used to monitor changes in the route and rate of degradation along with 14CO2 evolution (mineralization). Total microbial biomasses in both soils were significantly reduced for soils incubated in the flow-through apparatus, whereas only the Trevino soil's microbial biomass was significantly reduced as a result of storage. The microbial communities of both soils were significantly different as a result of storage as shown by discriminant analysis. In both soils, degradation rate, pathway of degradation, and mineralization of metsulfuron-methyl were significantly affected by storage compared to fresh soil. The half-life of metsulfuron-methyl increased significantly (P < 0.05) in the Trevino soil from 45 days (fresh) to 63 days (stored soil), whereas in the Fargo soil half-lives increased significantly (P < 0.05) from 23 days (fresh) to 29 days (soils stored for 6 months). In both soils, mineralization of [14C]metsulfuron-methyl was significantly (P < 0.05) higher in fresh soils compared to stored soils. The degradation pathways of metsulfuron-methyl changed with storage as evidenced by the loss of formation of one biologically derived metabolite (degradate) in stored soils compared to fresh soils.

Boundaries for biofilm formation: humidity and temperature

Environmental conditions which define boundaries for biofilm production could provide useful ecological information for biofilm models. A practical use of defined conditions could be applied to the high-level nuclear waste repository at Yucca Mountain. Data for temperature and humidity conditions indicate that decreases in relative humidity or increased temperature severely affect biofilm formation on three candidate canister metals.

Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples

We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption methods (bead mill homogenization and freeze-thaw lysis), and lysozyme digestion were evaluated based on the yield and molecular size of the recovered DNA. Pairwise comparisons of the nine extraction procedures revealed that bead mill homogenization with SDS combined with either chloroform or phenol optimized both the amount of DNA extracted and the molecular size of the DNA (maximum size, 16 to 20 kb). Neither lysozyme digestion before SDS treatment nor guanidine isothiocyanate treatment nor addition of Chelex 100 resin improved the DNA yields. Bead mill homogenization in a lysis mixture containing chloroform, SDS, NaCl, and phosphate-Tris buffer (pH 8) was found to be the best physical lysis technique when DNA yield and cell lysis efficiency were used as criteria. The bead mill homogenization conditions were also optimized for speed and duration with two different homogenizers. Recovery of high-molecular-weight DNA was greatest when we used lower speeds and shorter times (30 to 120 s). We evaluated four different DNA purification methods (silica-based DNA binding, agarose gel electrophoresis, ammonium acetate precipitation, and Sephadex G-200 gel filtration) for DNA recovery and removal of PCR inhibitors from crude extracts. Sephadex G-200 spin column purification was found to be the best method for removing PCR-inhibiting substances while minimizing DNA loss during purification. Our results indicate that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed by Sephadex G-200 column purification.

Factors limiting microbial growth and activity at a proposed high-level nuclear repository, yucca mountain, nevada

As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone.

Computer-Assisted Laser Scanning and Video Microscopy for Analysis of Cryptosporidium parvum Oocysts in Soil, Sediment, and Feces

A computer-assisted laser scanning microscope equipped for confocal laser scanning and color video microscopy was used to examine Cryptosporidium parvum oocysts in two agricultural soils, a barnyard sediment, and calf fecal samples. An agar smear technique was developed for enumerating oocysts in soil and barnyard sediment samples. Enhanced counting efficiency and sensitivity (detection limit, 5.2 x 10(sup2) oocysts(middot)g [dry weight](sup-1)) were achieved by using a semiautomatic counting procedure and confocal laser scanning microscopy to enumerate immunostained oocysts and fragments of oocysts in the barnyard sediment. An agarose-acridine orange mounting procedure was developed for high-resolution confocal optical sectioning of oocysts in soil. Stereo images of serial optical sections revealed the three-dimensional spatial relationships between immunostained oocysts and the acridine orange-stained soil matrix material. In these hydrated, pyrophosphate-dispersed soil preparations, oocysts were not found to be attached to soil particles. A fluorogenic dye permeability assay for oocyst viability (A. T. Campbell, L. J. Robertson, and H. V. Smith, Appl. Environ. Microbiol. 58:3488-3493, 1992) was modified by adding an immunostaining step after application of the fluorogenic dyes propidium iodide and 4(prm1),6-diamidino-2-phenylindole. Comparison of conventional color epifluorescence and differential interference contrast images on one video monitor with comparable black-and-white laser-scanned confocal images on a second monitor allowed for efficient location and interpretation of fluorescently stained oocysts in the soil matrix. This multi-imaging procedure facilitated the interpretation of the viability assay results by overcoming the uncertainties caused by matrix interference and background fluorescence.

Enumeration and biomass estimation of bacteria in aquifer microcosm studies by flow cytometry

Flow cytometry was used to enumerate and characterize bacteria from a sand column microcosm simulating aquifer conditions. Pure cultures of a species of Bacillus isolated from subsurface sediments or Bacillus megaterium were first evaluated to identify these organisms' characteristic histograms. Counting was then carried out with samples from the aquifer microcosms. Enumeration by flow cytometry was compared with more-traditional acridine orange direct counting. These two techniques gave statistically similar results. However, counting by flow cytometry, in this case, surveyed a sample size 700 times greater than did acridine orange direct counting (25 (mu)l versus 0.034 (mu)l) and required 1/10 the time (2 h versus 20 h). Flow cytometry was able to distinguish the same species of bacteria grown under different nutrient conditions, and it could distinguish changes in cell growth patterns, specifically single cell growth versus chained cell growth in different regions of an aquifer microcosm. A biomass estimate was calculated by calibrating the total fluorescence of a sample from a pure culture with the dry weight of a freeze-dried volume from the original pure culture. Growth conditions significantly affected histograms and biomass estimates, so the calibration was carried out with cells grown under conditions similar to those in the aquifer microcosm. Costs associated with using flow cytometry were minimal compared with the amount of time saved in counting cells and estimating biomass.

Monitoring deep subsurface microbiota for assessment of safe long-term nuclear waste disposal

Microbes with their resistance to heat and radioactivity, if present and metabolically active, could have major effects on the safety of nuclear waste disposal by posing potential problems in long-term containment. This paper reviews the applicability of the signature lipid biomarker (SLB) analysis in the quantitative assessment of the viable biomass, community composition, and nutritional/physiological status of the subsurface microbiota as it exists in situ in subsurface samples. The samples described in this review are not unlike those expected to be recovered from proposed deep subsurface disposal sites. Assessment of the microbial community ecology using SLB analysis can be utilized to predict potential problems engendered by microbial metabolic activities of these communities in breaching containment by microbially facilitated corrosion and in the potential for subsequent facilitated transport of nuclides into the environment. SLB analysis of the in situ microbial ecology can be utilized to monitor the feasibility of containment options in modeling tests at the specific disposal sites.Key words: nuclear waste, deep subsurface, microbiota, microbial corrosion, safe long-term storage, signature lipid biomarkers.