Linking bacterial diversity and geochemistry of uranium-contaminated groundwater.

To understand the link between bacterial diversity and geochemistry in uranium-contaminated groundwater, microbial communities were assessed based on clone libraries of 16S rDNA genes from the USDOE Oak Ridge Field Research Centre (FRC) site. Four groundwater wells (GW835, GW836, FW113-47 and FW215-49) with a wide range of pH (3 to 7), nitrate (44 to 23,400 mg L(-1)), uranium (0.73 to 60.

Extracellular hydrolytic enzyme activities of the heterotrophic microbial communities of the Rouge River: an approach to evaluate ecosystem response to urbanization.

The potential effects of urbanization on the bioavailability of dissolved organic carbon (DOC) were tested by determining the extracellular enzyme activities of the heterotrophic microbial communities of the Rouge River. The activities of 19 enzymes were monitored across two water samples (river water and groundwater) at different spatial and temporal scales. High phosphatase, esterase, and aminopeptidase activities was observed in site 9 (site most exposed to anthropogenic sources) showed higher concentrations of DOC compared to sites 1 and 8 (sites exposed to less anthropogenic sources), where moderate activities of diverse range of enzymes were observed.

Salt-adapted bacteria isolated from the Rouge River and potential for degradation of contaminants and biotechnological applications.

The current work extends the phenotypic and molecular characterization of the bacterial culture collection from the Rouge River to gain an understanding of the physiology of the strains and their potential for biotechnological applications. Phenotypic and molecular analyses were performed on six unique strains. Most of the strains tested for hydrolytic activities were positive for the production of enzymes, in contrast to previously described species that showed very little hydrolase activities.

Reduction of compost phytotoxicity during the process of decomposition.

Hog manure from windrows composted at different operating strategies was used in a bioassay to determine phytotoxicity. Twelve windows that differed in composting strategies (i.e.

Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River.

The heterotrophic microbial communities of the Rouge River were tracked using Biolog Ecoplates to understand the metabolic diversity at different temporal and spatial scales, and potential link to river pollution. Site less impacted by anthrophogenic sources (site 1), showed markedly lower metabolic diversity. The only substrates that were utilized in the water samples were carbohydrates.

Using terminal restriction fragment length polymorphism (T-RFLP) analysis to assess microbial community structure in compost systems.

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer.

Isolation and characterization of rhizobacteria from composts that suppress the severity of bacterial leaf spot of radish.

ABSTRACT Composts can induce systemic resistance in plants to disease. Unfortunately, the degree of resistance induced seems highly variable and the basis for this effect is not understood. In this work, only 1 of 79 potting mixes prepared with different batches of mature, stabilized composts produced from several different types of solid wastes suppressed the severity of bacterial leaf spot of radish caused by Xanthomonas campestris pv.

Diversity of sulfate-reducing genes (dsrAB) in sediments from Puget Sound.

The aims of this study were to characterize the population structure and diversity of sulfate-reducing bacteria (SRB) from three distinct sites at Puget Sound, and relate the biogeochemical properties of the sediments to the sulfate-reducer communities. The population composition and diversity of sulfate-reducing bacteria carrying dsrAB genes from surface Puget Sound sediments was investigated using a polymerase chain reaction-based cloning approach. Sediment cores were collected from three different locations: Carr Inlet (C1A), Shallow Bud Inlet (S1A), and Turning Basin (T1A).

Microbial community profiling and characterization of some heterotrophic bacterial isolates from river waters and shallow groundwater wells along the Rouge River, southeast Michigan.

This study was conducted to elucidate microbiological characteristics of river water and groundwater communities in order to improve our conceptual and predictive understanding of river and groundwater ecosystem processes, functioning and management. Rouge River bacterial communities from shallow groundwater and river water were screened using Biolog Ecoplates, which test for oxidation of selected carbon sources and by culturing heterotrophic bacteria. The isolates cultured from the samples were also characterized using the 16SrRNA gene-based approach.

Halophilic and halotolerant bacteria from river waters and shallow groundwater along the Rouge River of southeastern Michigan.

The use of sodium chloride to melt highway and road snow is believed to have a significant effect on the groundwater ecosystem of the rivers where the salt from the roads drain. As the river composition changes, the bacterial population also changes to favour those bacteria that are more suited to the higher salt concentrations. In this experiment, we surveyed the cultivable salt-loving organisms (halophiles) on three sites that encompass the Rouge River (Lotz; site 1, Lilly, site; 8, and Ford Field, site 9).

Diversity of biogeochemical cycling genes from Puget Sound sediments using DNA microarrays.

Oligonucleotide-based microarray permits the simultaneous analysis of thousands of genes on a single chip, so that a better picture of the interactions among thousands of genes can be investigated at the same time. Our oligo microchips contained 763 50-mer probes that scan the region of different functional genes encoding amoA, pmoA, nirS, nirK, nifH, and dsrAB. These genes code for key enzymes in the ecosystem processes of nitrification, methane oxidation, denitrification, nitrogen fixation and sulfur reduction, respectively.

Stability in a denitrifying fluidized bed reactor.

This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%.

Microbial community dynamics in manure composts based on 16S and 18S rDNA T-RFLP profiles.

Compost processing is assumed to be related to the microbial communities present. However, methods that will evaluate these relationships are not well understood. In this study, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to evaluate the diversity of PCR-amplified bacterial 16S and fungal 18S rDNA communities from manure composts at different stages of composting (initial [day 0], thermophilic [day 24], and mature [day 104]).

Microbiological parameters as indicators of compost maturity.

Aims: The objectives of this study were to determine the changes of microbial properties of pig manure collected from pens with different management strategies and composted using different turning and moisture regimes; relate their association with humification parameters and compost temperature; and identify the most suitable microbial indicators of compost maturity.

Methods And Results: Six different microbial parameters, including total bacterial count, oxygen consumption rate, ATP content, dehydrogenase activity, and microbial biomass C and N, along with humification parameters [humic acid (HA), fulvic acid (FA) and HA : FA ratio] and compost temperature were monitored during composting. Significant positive correlations were found between temperature and microbial properties, including O2 consumption rate, ATP content, dehydrogenase activity, and microbial biomass N.

Bacterial community profiles on feathers during composting as determined by terminal restriction fragment length polymorphism analysis of 16S rDNA genes.

Composting is one of the more economical and environmentally safe methods of recycling feather waste generated by the poultry industry, since 90% of the feather weight consists of crude keratin protein, and feathers contain 15% N. However, the keratin in waste feathers is resistant to biodegradation and may require the addition of bacterial inocula to enhance the degradation process during composting. Two keratin-degrading bacteria isolated from plumage of wild songbirds and identified as Bacillus licheneformis (OWU 1411T) and Streptomyces sp.

Composting of spent pig litter in turned and forced-aerated piles.

A study was carried out to compare the compositing efficiency of spent litter (a mixture of partially decomposed pig manure and sawdust) in turned and forced-aerated piles. Duplicate piles were built with manual turning (every 4 days) during composting, and duplicate piles were set up with forced aeration using an air pump. The present study demonstrated that the efficiency of composting in the turned and forced-aerated piles was similar.

Fate of nitrogen during composting of chicken litter.

Chicken litter (a mixture of chicken manure, wood shavings, waste feed, and feathers) was composted in forced-aeration piles to understand the changes and losses of nitrogen (N) during composting. During the composting process, the chemical [different N fractions, organic matter (OM), organic carbon (C), and C:N ratio], physical, and microbial properties of the chicken litter were examined. Cumulative losses and mass balances of N and organic matter were also quantified to determine actual losses during composting.

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.

Microarrays fabricated with oligonucleotides longer than 40 bp have been introduced for monitoring whole genome expression but have not been evaluated with environmental samples. To determine the potential of this type of microarray for environmental studies, a 50-mer oligonucleotide microarray was constructed using 763 genes involved in nitrogen cycling: nitrite reductase (nirS and nirK), ammonia monooxygenase (amoA), nitrogenase (nifH), methane monooxygenase (pmoA), and sulfite reductase (dsrAB) from public databases and our own sequence collections. The comparison of the sequences from pure cultures indicated that the developed microarrays could provide species-level resolution for analyzing microorganisms involved in nitrification, denitrification, nitrogen fixation, methane oxidation, and sulfite reduction.

Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico.

To understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the Pacific coast of Mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a PCR-based cloning approach. A total of 50 operational taxonomic units (OTUs) for nirK and 82 OTUs for nirS were obtained from all samples. Forty-four of the nirS clones and 31 of the nirK clones were sequenced; the levels of similarity of the nirS clones were 52 to 92%, and the levels of similarity of the nirS clones were 50 to 99%.

Evaluation of organic matter and nutrient composition of partially decomposed and composted spent pig litter.

Characterization of soil-applied organic material is necessary in order to clarify the nature of the organic matterand nutrients in it. In this study, the organic matter and nutrient contents of the spent pig litter (a mixture of partially decomposed pig manure and sawdust) was characterized before and after windrow composting to: (1) determine their changes during composting, and (2) assess the suitability of the composted spent litter as a soil amendment. Results demonstrated that the time required to reach maturity, and the composition of composted spent litter, depended on the chemical properties of the initial compost feedstock as well as the compost strategies used during composting.

Evolution of extracellular enzyme activities during manure composting.

Aims: The objectives of this work were to determine the extracellular enzyme profiles during composting, relate the activities of these enzymes to the changes in microbial population and compare the enzyme profiles between two manures.

Methods And Results: API ZYM assay was used to monitor the activities of 19 extracellular enzymes during poultry and pig manure composting. Results showed an overall increase in diversity and relative abundance of enzymes present.

Effects of bacterial inoculum and moisture adjustment on composting of pig manure.

Spent litter (a mixture of partially composted pig manure and sawdust) was taken from pig pens employing the pig-on-litter system with and without the addition of a commercial bacterial product (Odor control (OC)-organic fertilizers (OF)). A duplicate series of windrows was set up with spent litter which contained the bacterial product and a further duplicate series was set up with spent litter which did not contain the bacterial product. All four sets had their initial moisture content adjusted to 60% but one of each duplicate pair had its moisture content adjusted to 60% during the entire period of further composting in windrows.

Composting of spent pig litter at different seasonal temperatures in subtropical climate.

To investigate the effects of seasonal temperatures on the composting of spent pig-manure sawdust litter (spent litter), two sets of experiments were carried out: one during winter, the other during summer. Physicochemical and microbial parameters including temperature, pH, inorganic N, humification indicators (HA and FA), heavy metals (Cu and Zn), total aerobic heterotrophs, ATP content and dehydrogenase activity were measured to understand changes in the spent litter during composting. Results demonstrated that the composting was faster during summer than winter.