Search Results - (Author, Cooperation:B. B. Ward)

2013-07-28

American Association for the Advancement of Science (AAAS)

0036-8075

1095-9203

Biology

Chemistry and Pharmacology

Computer Science

Medicine

Natural Sciences in General

Physics

Anaerobiosis ; Bacteria/*metabolism ; Carbon Cycle ; *Denitrification ; Geologic Sediments/chemistry/microbiology ; Metabolic Networks and Pathways ; Nitrogen/*analysis ; Nitrogen Fixation ; *Oceans and Seas ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; Seawater/*chemistry/*microbiology

2015-06-06

American Association for the Advancement of Science (AAAS)

0036-8075

1095-9203

Biology

Chemistry and Pharmacology

Computer Science

Medicine

Natural Sciences in General

Physics

Animals ; *Greenhouse Effect ; *Nitrogen Cycle ; Nitrous Oxide/*chemistry ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/chemistry ; Seawater/*chemistry

2014-04-26

American Association for the Advancement of Science (AAAS)

0036-8075

1095-9203

Biology

Chemistry and Pharmacology

Computer Science

Medicine

Natural Sciences in General

Physics

Ammonium Compounds/analysis/metabolism ; Anaerobiosis ; Bacteria/metabolism ; Denitrification ; Nitrites/analysis/metabolism ; Nitrogen/*analysis/metabolism ; Nitrogen Cycle ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*analysis/metabolism ; *Seawater/chemistry/microbiology

1476-4687

Nature Archives 1869 - 2009

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

[Auszug] In order to reconcile the mesopelagic zone carbon budget, chemolithotrophic production of organic matter was proposed as a possible mechanism7. During the Vertex III sediment trap experiment, we had an opportunity to examine the possibility of bacterial chemolithotrophic production at a station, ...

Electronic Resource

1476-4687

Nature Archives 1869 - 2009

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

[Auszug] Fig. 1 Methane distribution in western Cariaco Basin during February and March 1986. Inset: expanded scale for surface layer. Different symbols represent different casts. Methane concentrations determined using vacuum extraction of dissolved gas from water sample23 followed by injection of 100 to ...

Electronic Resource

1432-072X

Denitrifying bacteria ; Nitrite reductase ; Restriction fragment length polymorphism ; Diversity

Springer Online Journal Archives 1860-2000

Biology

Abstract Sequence divergence in the ribosomal genes of known strains and isolates of aquatic denitrifying bacteria was investigated using restriction fragment length polymorphism (RFLP) analysis. The same cultures were characterized for their homology with antibody and gene probes for nitrite reductase (NiR), a key enzyme in the denitrification pathway, and for amplification with a set of polymerase chain reaction primers designed to amplify a portion of the NiR gene. The NiR probes were developed from Pseudomonas stutzeri (ATCC 14405) and several P. stutzeri strains were included in the analyses. The RFLP analysis clustered most of the P. stutzeri strains together, but detected considerable diversity within this group. Isolates from three aquatic environments exhibited within —and among — habitat diversity by RFLP. Hybridization with the NiR probes and amplification with the NiR primers were not correlated with the clustering of strains by rDNA RFLP analysis. The relationships among strains deduced from ribosomal DNA RFLP reflect heterogeneity within the P. stutzeri group and among other pseudomonads, and the patterns differ from those inferred from specificity of the NiR probes.

Electronic Resource

1432-072X

Key words Denitrifying bacteria ; Nitrite reductase ; Restriction fragment length polymorphism ; Diversity

Springer Online Journal Archives 1860-2000

Biology

Abstract Sequence divergence in the ribosomal genes of known strains and isolates of aquatic denitrifying bacteria was investigated using restriction fragment length polymorphism (RFLP) analysis. The same cultures were characterized for their homology with antibody and gene probes for nitrite reductase (NiR), a key enzyme in the denitrification pathway, and for amplification with a set of polymerase chain reaction primers designed to amplify a portion of the NiR gene. The NiR probes were developed from Pseudomonas stutzeri (ATCC 14405) and several P. stutzeri strains were included in the analyses. The RFLP analysis clustered most of the P. stutzeri strains together, but detected considerable diversity within this group. Isolates from three aquatic environments exhibited within – and among – habitat diversity by RFLP. Hybridization with the NiR probes and amplification with the NiR primers were not correlated with the clustering of strains by rDNA RFLP analysis. The relationships among strains deduced from ribosomal DNA RFLP reflect heterogeneity within the P. stutzeri group and among other pseudomonads, and the patterns differ from those inferred from specificity of the NiR probes.

Electronic Resource

1432-072X

Nitrosococcus oceanus ; Methane oxidation ; Kinetics of ammonia oxidation

Springer Online Journal Archives 1860-2000

Biology

Abstract The kinetics of ammonia oxidation and the ability of a marine ammonia-oxidizing bacterium, Nitrosococcus oceanus, to metabolize methane were investigated in semicontinuous batch culture. The effects of inhibitors (acetylene and nitrapyrin) and coreactants were determined in order to elucidate the behavior of the ammonia oxygenase enzyme in N. oceanus. Acetylene and nitrapyrin were potent inhibitors and their effects were not mitigated by increased ammonia concentrations. Oxygen concentration had the effect of a mixed-type inhibitor; reduced oxygen inhibited the rate or ammonia oxidation at high substrate concentration but may enhance the rate at low substrate concentrations. Substrate affinity in terms of NH 4 + increased (K m decreased) with increasing pH. Optimal pH was about 8. Methane inhibited ammonia oxidation; the interaction was not simple competitive inhibition and the presence of multiple active sites on the enzyme was indicated by the behaviour of the inhibited treatments. Half-saturation constants for methane (K i=6.6 μM) and ammonia (K m=8.1 μM) were similar. N. oceanus oxidized methanol and methane linearly over time, with CO2 and cell material being produced at approximately equal rates.

Electronic Resource

1432-184X

Springer Online Journal Archives 1860-2000

Biology

Abstract Methods designed to detect microorganisms involved in the biogeochemistry of nitrogen in the marine environment are rapidly being developed and deployed in ecological investigations. Probes based on phylogenetic sequences (usually rRNA) and those based on the sequences of functional genes or proteins have both been demonstrated in the nitrogen cycle. The most progress has been made for ammonia oxidizers; several sets of PCR primers have been described and their specificity may be optimized to allow detection of genetically and ecologically meaningful groups. For denitrifying bacteria, functional probes based on nitrite reductase show most promise. These approaches should complement the more familiar, but no less sophisticated, methods that focus on quantification of in situ transformation rates. Both approaches in combination will be useful in understanding regulation and environmental control of biogeochemical processes.

Electronic Resource

1432-184X

Springer Online Journal Archives 1860-2000

Biology

Abstract A strain-specific immunofluorescence assay for enumeration of a marine denitrifying bacterium was developed and applied in the marine environment. The polyclonal antiserum for Pseudomonas stutzeri (ATCC 14405) did not react with other pseudomonads, other heterotrophs, or autotrophic nitrifying strains. The abundance of P. stutzeri in the shallow water column of Monterey Bay was less than 0.1% of the total bacterial abundance and decreased with depth, whereas the total bacterial abundance was variable and nearly constant with depth. P. stutzeri was also detected in the sediments of a microbial mat from Tomales Bay. The relatively low contribution of P. stutzeri to the total bacterial abundance in both environments implies that it is not a major component of the heterotrophic assemblage. This conclusion appears to hold for most other strains for which specific assays have been applied in the marine environment. The isolation of several different denitrifying strains from local marine environments implies that the culturable population is quite diverse, even in the absence of different selective enrichment media. Thus, strain specific immunofluorescence is of limited use in quantifying functional groups of bacteria. Conversely, they provide specific information on the diversity of natural populations and their relation to culturable strains.

Electronic Resource

1432-184X

Springer Online Journal Archives 1860-2000

Biology

Abstract In pure culture, the marine ammonia oxidizer,Nitrosococcus oceanus, exhibits normal Michaelis Menten kinetics with respect to its primary substrate, ammonia.N. oceanus also exhibits a kinetic response to methane. In the absence of methane, oxidation of ammonia is first order with respect to ammonia concentration under atmospheric oxygen concentrations at seawater pH. In the presence of methane, ammonia oxidation is inhibited, and the amount of inhibition is related to the relative concentrations of methane and ammonia. Using semicontinuous batch cultures as a source of organisms for short-term kinetic experiments, I investigated the relationship between ammonia and methane oxidation inN. oceanus by varying the absolute and relative concentration of both substrates. Methane appeared to act as a substrate analogue, and its effect on ammonia oxidation was modeled as a permutation of competitive inhibition involving a cooperative enzyme system. Methane was oxidized byN. oceanus, even in the absence of measurable ammonia oxidation, but the process was inhibited at increasing methane concentrations. Of the two product pools analyzed, an average of 37% of methane oxidized was detected in particulate (cell) material and the remainder was detected in14CO2. The contribution of methane to total carbon assimilation varied with the ratio [CH4]/[NH3] and may be significant under substrate concentrations typical of a dilute aquatic environment.

Electronic Resource

1573-5117

denitrifying bacteria ; Antarctic bacteria ; immunofluorescence

Springer Online Journal Archives 1860-2000

Biology

Abstract Denitrifying bacterial strains were isolated from Lake Bonney,apermanently ice-covered and chemically stratified lake in theMcMurdo dry valley region of Antarctica, using complex mediaat4 °C. Three strains, identified as denitrifiers bytheirability to produce nitrous oxide using nitrate or nitrite as arespiratory substrate, were characterized as to theirtemperatureand salinity optima for aerobic growth in batch culture; allthreewere psychrophilic and moderately halophilic. Maximum growthratesof near 0.024 h−1 were measured for all three strains.Growthrates projected to occur at in situ temperature andsalinityimply generation times on the order of 100 h. Species specificpolyclonal antisera were prepared against two of the strains,ELB17 (from the east lobe of the lake at 17 m) and WLB20 (fromthewest lobe at 20 m). Both strains were subsequently detectedandenumerated in the lake using the antisera. ELB17 was presentinboth lobes below the chemocline, while WLB20 was present inthewest lobe below the chemocline but only in surface waters oftheeast lobe. These distributions are related to the observedchemicaldistributions which imply the occurrence of denitrification inthewest lobe of the lake and not in the east lobe.

Electronic Resource

1573-5117

nitrification ; ammonia–oxidizing bacteria ; amoA ; Antarctic lakes ; family and species specific PCR detection of nitrfying bacteria

Springer Online Journal Archives 1860-2000

Biology

Abstract Marked differences in the concentrations of major ions and cations, macronutrient chemistry and general trophic status exist among the lakes of the McMurdo dry valleys in Antarctica. These differences have been attributed to both variations in stream inputs and in situ lake processes (Priscu, 1995; Lizotte et al., 1996, Spigel and Priscu, 1996). This study examines the role of nitrifying bacteria in nitrogen transformations in these lakes. Applying two polymerase chain reaction (PCR) assays targeting the 16S rRNA genes of ammonia-oxidizing bacteria and the active site of the ammonia monooxygenase gene (amoA), the distribution of ammonia-oxidizers was examined in six Antarctic lakes: Lake Bonney, Lake Hoare, Lake Fryxell and Lake Joyce in the Taylor Valley, Lake Miers in the the Miers Valley and Lake Vanda in the Wright Valley. Using a two stage amplification procedure, ammonia-oxidizers from both the beta and gamma- subclasses of the Proteobacteria were detected and their relative abundances were determined in samples collected from all sites. Ammonia-oxidizers were detected in all lakes sampled. Members of the gamma subclass were only present in the saline lakes. In general, nitrifiers were most abundant at depths above the pycnocline and were usually associated with lower concentrations of NH4 and elevated concentrations of NO3 or NO2. The distribution of nitrifiers suggests that the primary N2O peak observed in most of the lakes was produced via nitrification. Preliminary data on the rate of nitrification (Priscu et al., 1996) support the occurrence of nitrification and the presence of nitrifiers at the depth intervals where nitrifiers were detected. In all lakes, except Lake Miers, the data indicate that nitrifying bacteria have an important role in the vertical distribution of nitrogen compounds in these systems.

Electronic Resource

1573-1561

Nitrosomonas europaea ; nitrification ; inhibition ; kinetics ; monoterpenes ; Sequoia sempervirens ; conifers ; nitrogen cycling

Springer Online Journal Archives 1860-2000

Biology

Chemistry and Pharmacology

Abstract Inhibition by allelochemicals, including monoterpenes, has been suggested as a factor in the extremely low nitrification rates observed in coastal redwood forests. Similarities between the molecular structure of known nitrification inhibitors and some conifer monoterpenes have been suggested as one reason for the inhibition of autotrophic nitrifiers by conifer monoterpenes. The effect of monolerpenes on nitrification rate and growth of Nitrosomonas europaea was examined in whole-cell pure culture experiments using the five most abundant monoterpenes in coastal redwood needles. These are (in order of decreasing concentration in the needles) limonene, α-pinenc, sabinene, myrcene, and γ-terpinene. Four of the five compounds significantly inhibited growth of N. europaea in batch culture experiments. Short-term kinetic studies of the two most inhibitory monoterpenes, limonene and α-pinene, were performed on whole cells to evaluate the mode of interaction between these chemicals and nitrification rates. Inhibition constants (K i) of limonene (38 μM) and α-pinene (95 μM) were determined. Lineweaver-Burk plots of nitrification in the presence of monoterpenes appear to fit a noncompetitive inhibition model; however, the mechanisms of inhibition may be more complex.

Electronic Resource