Ian Head | Newcastle University (original) (raw)
Papers by Ian Head
Journal of Analytical and Applied Pyrolysis, 2001
Pyrolysis-gas chromatography-mass spectrometry, in the presence of tetramethylammonium hydroxide ... more Pyrolysis-gas chromatography-mass spectrometry, in the presence of tetramethylammonium hydroxide (TMAH), was used in the molecular characterisation of lignin in wheat straw during its fungal degradation by Agaricus bisporus. The decayed wheat straw had a lower proportion of syringyl to guaiacyl derived moieties than its native counterpart. The ratio of methyl 3,4-dimethoxybenzoate to 3,4-dimethoxybenzaldehyde increased from 1.0 in native wheat straw to 6.4 following fungal degradation. Similarly the ratio of methyl 3,4,5-trimethoxybenzoate to 3,4,5-trimethoxybenzaldehyde increased from 1.6 in native wheat straw to 3.1 upon decay. The increase in both guaiacyl and syringyl acid to aldehyde ratios indicated that A. bisporus induces oxidative cleavage of lignin at the Ca Cb bonds. Both the threo-and erythro-isomers of 1-(3,4-dimethoxyphenyl)-1,2,3-trimethoxypropane decreased in intensity relative to other thermochemolysis products in degraded wheat straw. The increase in the ratio of methyl 3,4,-dimethoxybenzoate to the sum of 1-(3,4dimethoxyphenyl)-1,2,3-trimethoxypropane (threo-and erythro-isomers) from 1.0 in native wheat straw to 10.9 in A. bisporus decayed wheat straw confirmed that the fungus had cleaved alkyl side chains. Pyrolysis-gas chromatography-mass spectrometry in the presence of TMAH provides a sensitive method for tracking the oxidative degradation of lignin during the fungal decay of wheat straw.
Environmental Pollution, 2010
Denitrification is a process that reduces nitrogen levels in headwaters and other streams. We com... more Denitrification is a process that reduces nitrogen levels in headwaters and other streams. We compared nirS and nirK abundances with the absolute rate of denitrification, the longitudinal coefficient of denitrification (i.e., Kden, which represents optimal denitrification rates at given environmental conditions), and water quality in seven prairie streams to determine if nir-gene abundances explain denitrification activity. Previous work showed that absolute rates of denitrification correlate with nitrate levels; however, no correlation has been found for denitrification efficiency, which we hypothesise might be related to gene abundances. Water-column nitrate and soluble-reactive phosphorus levels significantly correlated with absolute rates of denitrification, but nir-gene abundances did not. However, nirS and nirK abundances significantly correlated with Kden, as well as phosphorus, although no correlation was found between Kden and nitrate. These data confirm that absolute denitrification rates are controlled by nitrate load, but intrinsic denitrification efficiency is linked to nirS and nirK gene abundances.
FEMS microbiology ecology, Jan 4, 2015
Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reac... more Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske-centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske-centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimised, following MIQE guidelines (Minimum Information for Publication of Quantitativ...
The ISME journal, Jan 17, 2014
Bacterial spores are widespread in marine sediments, including those of thermophilic, sulphate-re... more Bacterial spores are widespread in marine sediments, including those of thermophilic, sulphate-reducing bacteria, which have a high minimum growth temperature making it unlikely that they grow in situ. These Desulfotomaculum spp. are thought to be from hot environments and are distributed by ocean currents. Their cells and spores upper temperature limit for survival is unknown, as is whether they can survive repeated high-temperature exposure that might occur in hydrothermal systems. This was investigated by incubating estuarine sediments significantly above (40-80 °C) maximum in situ temperatures (∼23 °C), and with and without prior triple autoclaving. Sulphate reduction occurred at 40-60 °C and at 60 °C was unaffected by autoclaving. Desulfotomaculum sp. C1A60 was isolated and was most closely related to the thermophilic D. kuznetsovii(T) (∼96% 16S rRNA gene sequence identity). Cultures of Desulfotomaculum sp. C1A60, D. kuznetsovii(T)and D. geothermicum B2T survived triple autocla...
... consid-ering microbial populations as V or'K'strategists, with distinct colonisatio... more ... consid-ering microbial populations as V or'K'strategists, with distinct colonisation and survival characteristics (Graham & Curtis 2003) that ... principally members of the genera Nitrosospira and Nitrosomonas, in nitrification in a wide range of environments (Kowalchuk & Stephen ...
A laboratory scale reactor operated as a single sludge, denitrification-nitrification bioreactor ... more A laboratory scale reactor operated as a single sludge, denitrification-nitrification bioreactor (DNB), was fed a synthetic wastewater. The effect of the C/N ratio of the influent on the structure of beta-proteobacterial autotrophic ammonia-oxidizing bacterial (AOB) communities was determined by DGGE analysis of 16S rRNA gene fragments amplified using a range of AOB-selective primers. Fluorescence in situ hybridisation (FISH) was used to determine quantitative changes in the AOB communities. When operated at a C/N ratio of 2 the DNB was effective in nitrogen removal and nitrification was measured at approximately 1.0 mg NH4+-N/g dry wt/h. Altering the C/N ratio to 5 resulted in a 50% reduction in nitrification rates. Nitrification was restored to its original level when the C/N ratio was returned to 2. AOB were detected by DGGE analysis of samples from the DNB under all operating conditions but the changes in C/N ratio and nitrification rates were accompanied by changes in the community structure of the AOB. However, quantitative FISH analysis indicated that beta-proteobacterial AOB were only present in high numbers (ca. 10(8) cells/ml) under the original operating conditions with a C/N ratio of 2. Beta-proteobacterial AOB could not be detected by FISH when the C/N ratio was 5. When nitrification activity was restored by returning the C/N ratio to 2, beta-proteobacterial AOB were still not detected and it is likely that either beta-proteobacterial AOB were not responsible for ammonia oxidation or that beta-proteobacterial AOB that did not contain the target sites for the range of 4 AOB selective probes used, were present in the reactor.
Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleu... more Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleum reservoirs and anoxic environments contaminated with petroleum. There are several possible routes whereby hydrocarbons may be converted to methane: (i) complete oxidation of alkanes to H 2 and CO 2 , linked to methanogenesis from CO 2 reduction; (ii) oxidation of alkanes to acetate and H 2 , linked to acetoclastic methanogenesis and CO 2 reduction; (iii) oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction; (iv) oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis and (v) oxidation of alkanes to acetate alone, linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction. We have developed the concept of a 'window of opportunity' to evaluate the range of conditions under which each route is thermodynamically feasible. On this basis the largest window of opportunity is presented by the oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis. This contradicts field-based evidence that indicates that in petroleum rich environments acetoclastic methanogenesis is inhibited and that methanogenic CO 2 reduction is the predominant methanogenic process. Our analysis demonstrates that under those biological constraints oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction offers a greater window of opportunity than complete oxidation of alkanes to H 2 and CO 2 linked to methanogenic CO 2 reduction, and hence is the process most likely to occur. Thermodynamic constraints J Dolfing et al 443 The ISME Journal Thermodynamic constraints J Dolfing et al
Lab-scale reactors are commonly used to simulate full-scale plants as they permit the effects of ... more Lab-scale reactors are commonly used to simulate full-scale plants as they permit the effects of defined experimental perturbations to be evaluated. Ideally, lab- and full-scale reactors should possess similar microbial populations. To determine this we compared the diversity of the beta-proteobacterial autotrophic ammonia-oxidising bacteria (AOB) in a full-scale and lab-scale biological aerated filter (BAF) using PCR with AOB selective primers combined with denaturing gradient gel electrophoresis (DGGE). PCR amplified 16S rRNA gene fragments from the nitrification unit of the lab-and full-scale BAF were subjected to cloning and sequencing to determine the phylogenetic affiliation of the AOB. A high degree of comparability between the lab-and full-scale BAF was observed with respect to AOB populations. However minor differences were apparent. The importance of these minor constituents in the overall performance of the reactor is unknown. Nonetheless the lab-scale reactor in this study did appear to reflect the dominant AOB community within the full-scale equivalent.
In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of a... more In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ؎ 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure.
Nature Reviews Microbiology, 2007
It is the best of times for biofilm research. Systems biology approaches are providing new insigh... more It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept
Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under... more Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems.
Water Science and Technology, 1998
ABSTRACT The diversity of autotrophic ammonia-oxidizing bacteria (AOB) of the b-subdivision of th... more ABSTRACT The diversity of autotrophic ammonia-oxidizing bacteria (AOB) of the b-subdivision of the class Proteobacteria was investigated in a laboratory-scale denitrification-nitrification bioreactor (DNB) treating a synthetic waste stream. 16S ribosomal RNA (rRNA) gene sequences were amplified from DNA extracted from the oxic DNB sludge. Comparative analysis of the rRNA sequences revealed considerable diversity among the AOB-like sequences. The majority of sequences recovered were related to Nitrosomonas spp. but a smaller number of Nitrosospira-like sequences were obtained. Since different AOB may have different kinetic properties the high diversity of AOB, even in a simple laboratory biotreater treating a simple waste stream, has important implications for the operation of nitrifying wastewater treatment processes.
Water Science & Technology, 2009
This study reports an investigation of the effect of the anode surface area on the performance of... more This study reports an investigation of the effect of the anode surface area on the performance of a single chamber microbial fuel cell (SCMFC) based biosensor for measuring the organic content of wastewater. A packed bed of graphite granules was used as the anode. The surface area of the anode was changed by altering the granule bed thickness (0.3 cm and 1 cm). The anode surface area was found to play a role in the dynamic response of the system. For a granule bed thickness of 1 cm and with an external resistance of 500 V, the response time (defined as the time required to achieve 95% of the steady-state current) was reduced by approximately 65% in comparison to a SCMFC biosensor with a carbon cloth anode.
Water Research, 2009
Wastewater a b s t r a c t
Sedimentology, 2001
Silici®ed deposits, such as sinters, occur in several modern geothermal environments, but the mec... more Silici®ed deposits, such as sinters, occur in several modern geothermal environments, but the mechanisms of silici®cation (and crucially the role of microorganisms in their construction) are still largely unresolved. Detailed examination of siliceous sinter, in particular sections of microstromatolites growing at the Krisuvik hot spring, Iceland, reveals that biomineralization contributes a major component to the overall structure, with approximately half the sinter thickness attributed to silici®ed microorganisms. Almost all microorganisms observed under the scanning electron microscope (SEM) are mineralized, with epicellular silica ranging in thickness from < 5 lm coatings on individual cells, to regions where entire colonies are cemented together in an amorphous silica matrix tens of micrometres thick. Within the overall pro®le, there appears to be two very distinct types of laminae that alternate repeatedly throughout the microstromatolite:`microbial' layers are predominantly consisting of ®lamentous, intact, vertically aligned, biomineralized cyanobacteria, identi®ed as Calothrix and Fischerella sp.; and weakly laminated silica layers which appear to be devoid of any microbial component. The microbial layers commonly have a sharply de®ned base, overlying the weakly laminated silica, and a gradational upper surface merging into the weakly laminated silica. These cyclic laminations are probably explained by variations in microbial activity. Active growth during spring/ summer allows the microorganisms to keep pace with silici®cation, with the cell surfaces facilitating silici®cation, while during their natural slow growth phase in the dark autumn/winter months silici®cation exceeds the bacteria's ability to compensate (i.e. grow upwards). At this stage, the microbial colony is probably not essential to microstromatolite formation, with silici®cation presumably occurring abiogenically. When conditions once again become favourable for growth, recolonization of the solid silica surface by free-living bacteria occurs: cell motility is not responsible for the laminations. We have also observed that microbial populations within the microstromatolite, some several mm in depth, appear viable, i.e. they still have their pigmentation, the trichomes are not collapsed, cell walls are unbroken, cytoplasm is still present and they proved culturable. This suggests that the bulk of silici®cation occurred rapidly, probably while the cells were still alive. Surprisingly, however, measurements of light transmittance through sections of the microstromatolite revealed that photosynthetically active light (PAL) only transmitted through the uppermost 2 mm. Therefore the`deeper' microbial Sedimentology (2001) 48, 415±433 Ó 2001 International Association of Sedimentologists 415
Proceedings of the National Academy of Sciences, 2011
Nitrification is a core process in the global nitrogen cycle that is essential for the functionin... more Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, 14 CO 2 fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of 13 CO 2 , was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs. heterotrophy | physiology | modeling | ammonia monooxygenase
Philosophical Transactions of the Royal Society B: Biological Sciences, 2006
The extent of microbial diversity is an intrinsically fascinating subject of profound practical i... more The extent of microbial diversity is an intrinsically fascinating subject of profound practical importance. The term 'diversity' may allude to the number of taxa or species richness as well as their relative abundance. There is uncertainty about both, primarily because sample sizes are too small. Non-parametric diversity estimators make gross underestimates if used with small sample sizes on unevenly distributed communities. One can make richness estimates over many scales using small samples by assuming a species/taxa-abundance distribution. However, no one knows what the underlying taxa-abundance distributions are for bacterial communities. Latterly, diversity has been estimated by fitting data from gene clone libraries and extrapolating from this to taxa-abundance curves to estimate richness. However, since sample sizes are small, we cannot be sure that such samples are representative of the community from which they were drawn. It is however possible to formulate, and calibrate, models that predict the diversity of local communities and of samples drawn from that local community. The calibration of such models suggests that migration rates are small and decrease as the community gets larger. The preliminary predictions of the model are qualitatively consistent with the patterns seen in clone libraries in 'real life'. The validation of this model is also confounded by small sample sizes. However, if such models were properly validated, they could form invaluable tools for the prediction of microbial diversity and a basis for the systematic exploration of microbial diversity on the planet.
Nature Reviews Microbiology, 2007
| It is the best of times for biofilm research. Systems biology approaches are providing new insi... more | It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.
Journal of Analytical and Applied Pyrolysis, 2001
Pyrolysis-gas chromatography-mass spectrometry, in the presence of tetramethylammonium hydroxide ... more Pyrolysis-gas chromatography-mass spectrometry, in the presence of tetramethylammonium hydroxide (TMAH), was used in the molecular characterisation of lignin in wheat straw during its fungal degradation by Agaricus bisporus. The decayed wheat straw had a lower proportion of syringyl to guaiacyl derived moieties than its native counterpart. The ratio of methyl 3,4-dimethoxybenzoate to 3,4-dimethoxybenzaldehyde increased from 1.0 in native wheat straw to 6.4 following fungal degradation. Similarly the ratio of methyl 3,4,5-trimethoxybenzoate to 3,4,5-trimethoxybenzaldehyde increased from 1.6 in native wheat straw to 3.1 upon decay. The increase in both guaiacyl and syringyl acid to aldehyde ratios indicated that A. bisporus induces oxidative cleavage of lignin at the Ca Cb bonds. Both the threo-and erythro-isomers of 1-(3,4-dimethoxyphenyl)-1,2,3-trimethoxypropane decreased in intensity relative to other thermochemolysis products in degraded wheat straw. The increase in the ratio of methyl 3,4,-dimethoxybenzoate to the sum of 1-(3,4dimethoxyphenyl)-1,2,3-trimethoxypropane (threo-and erythro-isomers) from 1.0 in native wheat straw to 10.9 in A. bisporus decayed wheat straw confirmed that the fungus had cleaved alkyl side chains. Pyrolysis-gas chromatography-mass spectrometry in the presence of TMAH provides a sensitive method for tracking the oxidative degradation of lignin during the fungal decay of wheat straw.
Environmental Pollution, 2010
Denitrification is a process that reduces nitrogen levels in headwaters and other streams. We com... more Denitrification is a process that reduces nitrogen levels in headwaters and other streams. We compared nirS and nirK abundances with the absolute rate of denitrification, the longitudinal coefficient of denitrification (i.e., Kden, which represents optimal denitrification rates at given environmental conditions), and water quality in seven prairie streams to determine if nir-gene abundances explain denitrification activity. Previous work showed that absolute rates of denitrification correlate with nitrate levels; however, no correlation has been found for denitrification efficiency, which we hypothesise might be related to gene abundances. Water-column nitrate and soluble-reactive phosphorus levels significantly correlated with absolute rates of denitrification, but nir-gene abundances did not. However, nirS and nirK abundances significantly correlated with Kden, as well as phosphorus, although no correlation was found between Kden and nitrate. These data confirm that absolute denitrification rates are controlled by nitrate load, but intrinsic denitrification efficiency is linked to nirS and nirK gene abundances.
FEMS microbiology ecology, Jan 4, 2015
Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reac... more Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske-centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske-centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimised, following MIQE guidelines (Minimum Information for Publication of Quantitativ...
The ISME journal, Jan 17, 2014
Bacterial spores are widespread in marine sediments, including those of thermophilic, sulphate-re... more Bacterial spores are widespread in marine sediments, including those of thermophilic, sulphate-reducing bacteria, which have a high minimum growth temperature making it unlikely that they grow in situ. These Desulfotomaculum spp. are thought to be from hot environments and are distributed by ocean currents. Their cells and spores upper temperature limit for survival is unknown, as is whether they can survive repeated high-temperature exposure that might occur in hydrothermal systems. This was investigated by incubating estuarine sediments significantly above (40-80 °C) maximum in situ temperatures (∼23 °C), and with and without prior triple autoclaving. Sulphate reduction occurred at 40-60 °C and at 60 °C was unaffected by autoclaving. Desulfotomaculum sp. C1A60 was isolated and was most closely related to the thermophilic D. kuznetsovii(T) (∼96% 16S rRNA gene sequence identity). Cultures of Desulfotomaculum sp. C1A60, D. kuznetsovii(T)and D. geothermicum B2T survived triple autocla...
... consid-ering microbial populations as V or'K'strategists, with distinct colonisatio... more ... consid-ering microbial populations as V or'K'strategists, with distinct colonisation and survival characteristics (Graham & Curtis 2003) that ... principally members of the genera Nitrosospira and Nitrosomonas, in nitrification in a wide range of environments (Kowalchuk & Stephen ...
A laboratory scale reactor operated as a single sludge, denitrification-nitrification bioreactor ... more A laboratory scale reactor operated as a single sludge, denitrification-nitrification bioreactor (DNB), was fed a synthetic wastewater. The effect of the C/N ratio of the influent on the structure of beta-proteobacterial autotrophic ammonia-oxidizing bacterial (AOB) communities was determined by DGGE analysis of 16S rRNA gene fragments amplified using a range of AOB-selective primers. Fluorescence in situ hybridisation (FISH) was used to determine quantitative changes in the AOB communities. When operated at a C/N ratio of 2 the DNB was effective in nitrogen removal and nitrification was measured at approximately 1.0 mg NH4+-N/g dry wt/h. Altering the C/N ratio to 5 resulted in a 50% reduction in nitrification rates. Nitrification was restored to its original level when the C/N ratio was returned to 2. AOB were detected by DGGE analysis of samples from the DNB under all operating conditions but the changes in C/N ratio and nitrification rates were accompanied by changes in the community structure of the AOB. However, quantitative FISH analysis indicated that beta-proteobacterial AOB were only present in high numbers (ca. 10(8) cells/ml) under the original operating conditions with a C/N ratio of 2. Beta-proteobacterial AOB could not be detected by FISH when the C/N ratio was 5. When nitrification activity was restored by returning the C/N ratio to 2, beta-proteobacterial AOB were still not detected and it is likely that either beta-proteobacterial AOB were not responsible for ammonia oxidation or that beta-proteobacterial AOB that did not contain the target sites for the range of 4 AOB selective probes used, were present in the reactor.
Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleu... more Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleum reservoirs and anoxic environments contaminated with petroleum. There are several possible routes whereby hydrocarbons may be converted to methane: (i) complete oxidation of alkanes to H 2 and CO 2 , linked to methanogenesis from CO 2 reduction; (ii) oxidation of alkanes to acetate and H 2 , linked to acetoclastic methanogenesis and CO 2 reduction; (iii) oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction; (iv) oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis and (v) oxidation of alkanes to acetate alone, linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction. We have developed the concept of a 'window of opportunity' to evaluate the range of conditions under which each route is thermodynamically feasible. On this basis the largest window of opportunity is presented by the oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis. This contradicts field-based evidence that indicates that in petroleum rich environments acetoclastic methanogenesis is inhibited and that methanogenic CO 2 reduction is the predominant methanogenic process. Our analysis demonstrates that under those biological constraints oxidation of alkanes to acetate and H 2 , linked to syntrophic acetate oxidation and methanogenesis from CO 2 reduction offers a greater window of opportunity than complete oxidation of alkanes to H 2 and CO 2 linked to methanogenic CO 2 reduction, and hence is the process most likely to occur. Thermodynamic constraints J Dolfing et al 443 The ISME Journal Thermodynamic constraints J Dolfing et al
Lab-scale reactors are commonly used to simulate full-scale plants as they permit the effects of ... more Lab-scale reactors are commonly used to simulate full-scale plants as they permit the effects of defined experimental perturbations to be evaluated. Ideally, lab- and full-scale reactors should possess similar microbial populations. To determine this we compared the diversity of the beta-proteobacterial autotrophic ammonia-oxidising bacteria (AOB) in a full-scale and lab-scale biological aerated filter (BAF) using PCR with AOB selective primers combined with denaturing gradient gel electrophoresis (DGGE). PCR amplified 16S rRNA gene fragments from the nitrification unit of the lab-and full-scale BAF were subjected to cloning and sequencing to determine the phylogenetic affiliation of the AOB. A high degree of comparability between the lab-and full-scale BAF was observed with respect to AOB populations. However minor differences were apparent. The importance of these minor constituents in the overall performance of the reactor is unknown. Nonetheless the lab-scale reactor in this study did appear to reflect the dominant AOB community within the full-scale equivalent.
In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of a... more In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ؎ 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure.
Nature Reviews Microbiology, 2007
It is the best of times for biofilm research. Systems biology approaches are providing new insigh... more It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept
Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under... more Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems.
Water Science and Technology, 1998
ABSTRACT The diversity of autotrophic ammonia-oxidizing bacteria (AOB) of the b-subdivision of th... more ABSTRACT The diversity of autotrophic ammonia-oxidizing bacteria (AOB) of the b-subdivision of the class Proteobacteria was investigated in a laboratory-scale denitrification-nitrification bioreactor (DNB) treating a synthetic waste stream. 16S ribosomal RNA (rRNA) gene sequences were amplified from DNA extracted from the oxic DNB sludge. Comparative analysis of the rRNA sequences revealed considerable diversity among the AOB-like sequences. The majority of sequences recovered were related to Nitrosomonas spp. but a smaller number of Nitrosospira-like sequences were obtained. Since different AOB may have different kinetic properties the high diversity of AOB, even in a simple laboratory biotreater treating a simple waste stream, has important implications for the operation of nitrifying wastewater treatment processes.
Water Science & Technology, 2009
This study reports an investigation of the effect of the anode surface area on the performance of... more This study reports an investigation of the effect of the anode surface area on the performance of a single chamber microbial fuel cell (SCMFC) based biosensor for measuring the organic content of wastewater. A packed bed of graphite granules was used as the anode. The surface area of the anode was changed by altering the granule bed thickness (0.3 cm and 1 cm). The anode surface area was found to play a role in the dynamic response of the system. For a granule bed thickness of 1 cm and with an external resistance of 500 V, the response time (defined as the time required to achieve 95% of the steady-state current) was reduced by approximately 65% in comparison to a SCMFC biosensor with a carbon cloth anode.
Water Research, 2009
Wastewater a b s t r a c t
Sedimentology, 2001
Silici®ed deposits, such as sinters, occur in several modern geothermal environments, but the mec... more Silici®ed deposits, such as sinters, occur in several modern geothermal environments, but the mechanisms of silici®cation (and crucially the role of microorganisms in their construction) are still largely unresolved. Detailed examination of siliceous sinter, in particular sections of microstromatolites growing at the Krisuvik hot spring, Iceland, reveals that biomineralization contributes a major component to the overall structure, with approximately half the sinter thickness attributed to silici®ed microorganisms. Almost all microorganisms observed under the scanning electron microscope (SEM) are mineralized, with epicellular silica ranging in thickness from < 5 lm coatings on individual cells, to regions where entire colonies are cemented together in an amorphous silica matrix tens of micrometres thick. Within the overall pro®le, there appears to be two very distinct types of laminae that alternate repeatedly throughout the microstromatolite:`microbial' layers are predominantly consisting of ®lamentous, intact, vertically aligned, biomineralized cyanobacteria, identi®ed as Calothrix and Fischerella sp.; and weakly laminated silica layers which appear to be devoid of any microbial component. The microbial layers commonly have a sharply de®ned base, overlying the weakly laminated silica, and a gradational upper surface merging into the weakly laminated silica. These cyclic laminations are probably explained by variations in microbial activity. Active growth during spring/ summer allows the microorganisms to keep pace with silici®cation, with the cell surfaces facilitating silici®cation, while during their natural slow growth phase in the dark autumn/winter months silici®cation exceeds the bacteria's ability to compensate (i.e. grow upwards). At this stage, the microbial colony is probably not essential to microstromatolite formation, with silici®cation presumably occurring abiogenically. When conditions once again become favourable for growth, recolonization of the solid silica surface by free-living bacteria occurs: cell motility is not responsible for the laminations. We have also observed that microbial populations within the microstromatolite, some several mm in depth, appear viable, i.e. they still have their pigmentation, the trichomes are not collapsed, cell walls are unbroken, cytoplasm is still present and they proved culturable. This suggests that the bulk of silici®cation occurred rapidly, probably while the cells were still alive. Surprisingly, however, measurements of light transmittance through sections of the microstromatolite revealed that photosynthetically active light (PAL) only transmitted through the uppermost 2 mm. Therefore the`deeper' microbial Sedimentology (2001) 48, 415±433 Ó 2001 International Association of Sedimentologists 415
Proceedings of the National Academy of Sciences, 2011
Nitrification is a core process in the global nitrogen cycle that is essential for the functionin... more Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, 14 CO 2 fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of 13 CO 2 , was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs. heterotrophy | physiology | modeling | ammonia monooxygenase
Philosophical Transactions of the Royal Society B: Biological Sciences, 2006
The extent of microbial diversity is an intrinsically fascinating subject of profound practical i... more The extent of microbial diversity is an intrinsically fascinating subject of profound practical importance. The term 'diversity' may allude to the number of taxa or species richness as well as their relative abundance. There is uncertainty about both, primarily because sample sizes are too small. Non-parametric diversity estimators make gross underestimates if used with small sample sizes on unevenly distributed communities. One can make richness estimates over many scales using small samples by assuming a species/taxa-abundance distribution. However, no one knows what the underlying taxa-abundance distributions are for bacterial communities. Latterly, diversity has been estimated by fitting data from gene clone libraries and extrapolating from this to taxa-abundance curves to estimate richness. However, since sample sizes are small, we cannot be sure that such samples are representative of the community from which they were drawn. It is however possible to formulate, and calibrate, models that predict the diversity of local communities and of samples drawn from that local community. The calibration of such models suggests that migration rates are small and decrease as the community gets larger. The preliminary predictions of the model are qualitatively consistent with the patterns seen in clone libraries in 'real life'. The validation of this model is also confounded by small sample sizes. However, if such models were properly validated, they could form invaluable tools for the prediction of microbial diversity and a basis for the systematic exploration of microbial diversity on the planet.
Nature Reviews Microbiology, 2007
| It is the best of times for biofilm research. Systems biology approaches are providing new insi... more | It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.