Papers by Annette Bollmann
Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2 . Fo... more Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2 . For example, nitrifying and denitrifying bacteria respond strongly to changes in soil water and O 2 availability by producing more or less of the atmospheric trace gases NO and N 2 O. Consumption of NO also responds to O 2 availability, as it may proceed by reductive or oxidative pathways. Complete depletion of O 2 in the soil (e.g. flooding of rice fields) results in the sequential change of the redox processes until CH 4 is emitted into the atmosphere. Driving forces are the availability of electron donors (organic substrates) and electron acceptors (mainly the content of iron). It is interesting to note that CH 4 production starts almost instantaneously after flooding, then comes to a halt as soon as competing redox processes (iron and sulfate reduction) start, and finally resumes vigorously when ferric iron and sulfate are depleted. Drainage of submerged fields, even short-term, regene...
Soil Biology and Biochemistry, 1997
The acetylene inhibition technique is a widely used method to measure denitrification rates in so... more The acetylene inhibition technique is a widely used method to measure denitrification rates in soil. This technique is based on the inhibition of the N2O reductase with high concentrations of acetylene (about 10%). We tested possible artifacts created by using this technique under oxic conditions. Parts per billion concentrations of NO, an intermediate of the denitrification, were converted to NO2
Life, 2015
In their natural habitats, microorganisms are often exposed to periods of starvation if their sub... more In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies.
Journal of Bacteriology, 2011
Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) ... more Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates in comparison to strains in Nitrosomonas cluster 7 that includes Nitrosomonas europaea and Nitrosomonas
Methods in enzymology, 2011
Ammonia-oxidizing microorganisms (AOM) generate their energy by the oxidation of ammonia (NH(3)) ... more Ammonia-oxidizing microorganisms (AOM) generate their energy by the oxidation of ammonia (NH(3)) to nitrite (NO(2)(-)). This process can be carried out by ammonia-oxidizing bacteria (AOB) as well as by the recently discovered ammonia-oxidizing archaea (AOA). In the past, AOB were enriched in batch cultures, often in the presence of rather high concentrations of NH(4)(+). Here, we describe methods to enrich, isolate, and investigate the basic physiology of AOB and AOA with emphasis on those that are adapted to low NH(4)(+) concentrations. The methods described include enrichment of AOA and AOB in batch cultures and of AOB in continuous cultures, the isolation of AOA by serial dilution and AOB by pour plates or dilution to extinction, and techniques to determine growth and activity of the AOA and AOB. Finally, we incorporated a section with Appendix about the identification of AOA and AOB as well as the measurement of the different inorganic nitrogen species.
Genome Announcements, 2013
Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsur... more Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here. Citation Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD. 2013. Draft genome sequence for Caulobacter sp. strain OR37, a bacterium tolerant to heavy metals. Genome Announc. 1(3):e00322-13.
Genome Announcements, 2013
Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from subsurfa... more Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. A member of this genus has been described as a potential bioremediation agent. Strain OR214 is tolerant to various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present its draft genome sequence here. Citation Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD. 2013. Draft genome sequence for Ralstonia sp. strain OR214, a bacterium with potential for bioremediation. Genome Announc. 1(3):e00321-13.
Standards in genomic sciences, 2013
Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the ... more Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.
Soil Biology and Biochemistry, 1997
We used the acetylene inhibition technique to measure the denitrification rates, the rates of gro... more We used the acetylene inhibition technique to measure the denitrification rates, the rates of gross production or net release of NO by denitrification (NOD), and the rates of net release of N2O by denitrification (N2OD) in 29 different soils. The denitrification rates were measured by accumulation of N2O in the presence of 10 kPa acetylene. The rates of NOD and
Sensors and Actuators B: Chemical, 2005
ABSTRACT An ammonium biosensor based on bacterial oxidation of ammonia with oxygen was constructe... more ABSTRACT An ammonium biosensor based on bacterial oxidation of ammonia with oxygen was constructed. The biosensor contained an internal oxygen reservoir from which oxygen was supplied to the biomass of ammonia oxidizing bacteria (AOB). The biosensor was thus designed to have best performance under ambient anoxic conditions. An oxygen microsensor was used to monitor the internal oxygen gradient. Due to the ammonia-oxidizing and respiratory activity of the AOB the signal from this oxygen microsensor was proportional to the ambient ammonium concentration in a range of 0–200 μM. Oxygen in the environment interfered with the reading, but it was in principle possible to compensate for a constant oxygen concentration in the analyzed medium. An increase in pH from 6 to 8.5 increased the sensitivity, while a range of chemicals affected the signal in various ways. A total of four biosensors were constructed, and one exhibited a lifetime of >2 months. Sensors containing bacteria that were starved for ammonium could be revived within 2 days by placing them in ammonium-containing medium. The 90% response times of the sensors were about 2 min, and the difference in signal between vigorously stirred and stagnant medium corresponded to about 10 μM NH4+ within the linear range. A sensor was tested in a wastewater treatment plant. The sensor signal during the anoxic periods corresponded well to the concentration of NH4+ analyzed by colorimetry.
Reviews in Environmental Science and Bio/Technology, 2002
In order to meet increasingly stringent European discharge standards, new applications and contro... more In order to meet increasingly stringent European discharge standards, new applications and control strategies for the sustainable removal of ammonia from wastewater have to be implemented. In this paper we discuss a nitrogen removal system based on the processes of partial nitrification and anoxic ammonia oxidation (anammox). The anammox process offers great opportunities to remove ammonia in fully autotrophic systems with biomass retention. No organic carbon is needed in such nitrogen removal system, since ammonia is used as electron donor for nitrite reduction. The nitrite can be produced from ammonia in oxygen-limited biofilm systems or in continuous processes without biomass retention. For successful implementation of the combined processes, accurate biosensors for measuring ammonia and nitrite concentrations, insight in the complex microbial communities involved, and new control strategies have to be developed and evaluated.
PLoS ONE, 2014
Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AO... more Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso-to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyrosequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.
Plant Physiology and Biochemistry, 2013
Other uses, including reproduction and distribution, or selling or licensing copies, or posting t... more Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited.
Journal of Microbiological Methods, 2008
The approach of growing microorganisms in situ, or in a simulated natural environment is appealin... more The approach of growing microorganisms in situ, or in a simulated natural environment is appealing, and different versions of it have been described by several groups. The major difficulties with these approaches are that they are not selective for actinomycetesa group of grampositive bacteria well known as a rich source of antibiotics. In order to efficiently access actinomycetes, a trap for specifically capturing and cultivating these microorganisms in situ has been developed, based on the ability of these bacteria to form hyphae and penetrate solid environments. The trap is formed by two semi-permeable membranes (0.2-0.6 μm pore-size bottom membrane and 0.03 μm pore-size top membrane) glued to a plastic washer with sterile agar or gellan gum inside. The trap is placed on top of soil, and filamentous microorganisms selectively penetrate into the device and form colonies. Decreasing the size of the pores of the lower membrane to 0.2 μm restricted penetration of fungi. The trap produced more filamentous actinobacteria, and a higher variety of them, as compared to a conventional Petri dish cultivation from the same soil sample. Importantly, the trap cultivation resulted in the isolation of unusual and rare actinomycetes.
Journal of Bacteriology, 2011
Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) ... more Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates in comparison to strains in Nitrosomonas cluster 7 that includes Nitrosomonas europaea and Nitrosomonas eutropha.
Global Change Biology, 1998
The availability of O 2 is believed to be one of the main factors regulating nitrification and de... more The availability of O 2 is believed to be one of the main factors regulating nitrification and denitrification and the release of NO and N 2 O.
FEMS Microbiology Ecology, 2000
Until now enrichments of ammonia-oxidizing bacteria from natural ammonium-limited environments ha... more Until now enrichments of ammonia-oxidizing bacteria from natural ammonium-limited environments have been performed mainly in the presence of much higher ammonia concentrations than those present in the natural environment and many have resulted in the enrichment and isolation of environmentally less important bacteria. Therefore, we used continuous cultures to enrich ammonia-oxidizing bacteria at growth-limiting ammonium concentrations of around 5 WM from the root zone of the macrophyte Glyceria maxima from the lake Drontermeer (The Netherlands). Molecular analysis at the end of the enrichment experiments showed that all continuous cultures consisted of Nitrosomonas cluster 6a, which comprises also Nitrosomonas ureae and Nitrosomonas oligotropha. This was independent of whether Nitrosomonas-or Nitrosospira-like bacteria were dominant in the inoculum. Thus all known ammonia-oxidizing bacteria belonging to Nitrosomonas cluster 6a are able to grow at very low ammonium concentrations. ß
FEMS Microbiology Ecology, 2000
In the Completely Autotrophic Nitrogen removal Over Nitrite (CANON) process, aerobic and anaerobi... more In the Completely Autotrophic Nitrogen removal Over Nitrite (CANON) process, aerobic and anaerobic ammonia oxidizing bacteria cooperate to remove ammonia in one oxygen-limited reactor. Kinetic studies, microsensor analysis, and fluorescence in situ hybridization on CANON biomass showed a partial differentiation of processes and organisms within and among aggregates. Under normal oxygen-limited conditions ($5 lM O 2 ), aerobic ammonia oxidation (nitrification) was restricted to an outer shell (<100 lm) while anaerobic ammonia oxidation (anammox) was found in the central anoxic parts. Larger type aggregates (>500 lm) accounted for 68% of the anammox potential whereas 65% of the nitrification potential was found in the smaller aggregates (<500 lm). Analysis with O 2 and NO À 2 microsensors showed that the thickness of the activity zones varied as a function of bulk O 2 and NO À 2 concentrations and flow rate.
Estuarine, Coastal and Shelf Science, 2010
... Desulfococcus genera (Fig. 2), with sulfur-based metabolisms. The first hint of the potential... more ... Desulfococcus genera (Fig. 2), with sulfur-based metabolisms. The first hint of the potential metabolic role of the Group I Crenarchaeota came from two independent metagenomic studies. Venter et al. (2004) reported the presence ...
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Papers by Annette Bollmann