Christiansen EA. 1979. The Wisconsinan deglaciation of southern Saskatchewan and adjacent areas. Canadian Journal of Earth Science 16: 913-938.
This author describes in considerable detail the process of deglaciation that occurred at the end of the last glacial maximum from about 17 000 years ago, as it occurs to Saskatchewan. Major geological features and patterns of melt-water drainage led to the inclusion of nearby parts of Alberta, Manitoba, Montana, and North Dakota in the analysis. Patterns during the deglaciation were identified by glacial landforms, many of which are apparent only from aerial photographs, with sample analysis in the lab including radio-carbon dating.
The period from 17 000 years to 10 000 years ago is divided into 9 phases corresponding to periods of rapid glacial retreat or temporary stasis or glacial advance. By 10 000 years ago the ice sheet that had covered nearly the entire province had retreated towards Hudson Bay and covered only a small part of the north of Saskatchewan. Glacial lakes formed from meltwater and from water flowing from the west (presumably sourced from glaciers in the Rocky mountains), sometimes reaching enormous sizes; these lakes were bordered by the glacier’s edge, and connected to each other via spillways that often carved large channels from the plains; the east-west valleys of southern Saskatchewan such as the Qu’Appelle valley are the remains of such spillways. Modern river systems such as the Saskatchewan River and the Churchill River formed during the glacial retreat, occupying low areas and spillway remnants.
The rate of deglaciation varied considerably over the studied 7 000 years, generally accelerating from about 150 m / yr to around 275 m / yr, though with frequent pauses, occasional re-advances, and variation across the glacial edge. The evidence from glacial lake-edge movements and depth patterns suggests the ice sheet melted fastest initially, but with the slowest retreat at that time indicating the sheet first thinned, and then retreated, especially around newly-uncovered Nunataks where the underlying land formed highlands.
This paper was on the suggested reading list for the course SLSC 834 in August 2010, but it is also personally interesting in describing Pleistocene events in areas I visit during Sunday drives across the center of the province.
Thursday, August 19, 2010
Tuesday, August 17, 2010
Wilkinson et al. 2009
Wilkinson MT, Richards PJ, Humphreys GS. 2009. Breaking ground: Pedological, geological, and ecological implications of soil bioturbation. Earth-Science Reviews 97: 257-272.
These authors describe the process of bioturbation in soils, and the roles of various major groups of organisms, especially animals, responsible for bioturbation. Through mixing and surface-mounding, bioturbation sorts, buries, and transports soil and soil components such as organic matter. Bioturbation also interacts with abiotic processes, particularly those involving surface water inputs and movements, to create net effects on soil movement and sorting.
There is a great deal of detail in the description of various sub-processes and rates, as well as some urging for more detailed studies of these phenomena. This paper is required reading for the course SLSC 834, in August 2010.
These authors describe the process of bioturbation in soils, and the roles of various major groups of organisms, especially animals, responsible for bioturbation. Through mixing and surface-mounding, bioturbation sorts, buries, and transports soil and soil components such as organic matter. Bioturbation also interacts with abiotic processes, particularly those involving surface water inputs and movements, to create net effects on soil movement and sorting.
There is a great deal of detail in the description of various sub-processes and rates, as well as some urging for more detailed studies of these phenomena. This paper is required reading for the course SLSC 834, in August 2010.
Monday, August 16, 2010
Johnson et al. 2005
Johnson DL, Domier JEJ, Johnson DN. 2005. Reflections on the nature of soil and its biomantle. Annals of the Association of American Geographers 95: 11-31.
These authors advocate a new paradigm to underlie studies of soil science and related fields, based on increased recognition of processes occurring in and responsible for the production of the “biomantle”, the upper layer of soil composed of and formed by the actions of organisms. Many of these processes are based on movements of soil and soil components, and so are dominated by animals, especially active burrowers that are responsible for large vertical movements of soil in some environments. The biomantle is defined as being composed of “biofabric”, or materials that owe their existence to the actions of organisms, from the bodies of these organisms themselves, to the materials released by the organisms, to the minerals created by biological processes, to the voids created by their movements and the gases filling those voids released by their metabolisms.
These authors trace their ideas from the writings of Darwin, particularly his final work involving the activity of worms in “vegetable mould”, a late-18th century term for what we now call soil.
A biomantle layer, residing chiefly in the A horizon (or topsoil) can be more easily recognized in some landscapes than others. Humid tropical soils especially may show very thick and distinct biomantles, in two layers. The upper, thicker layer is composed of relatively fine materials, resting on a basal layer of coarser material; this basal layer is referred to here as the stonelayer. Below the stonelayer is non-biomantle, typically a B horizon (or subsoil). The hypothesized process creating this two-layer biomantle is the action of “conveyor belt” animals, especially termites that carry small particles upwards but are unable to move larger stones, thus eventually sorting the soil mineral material.
In other soils, such as loess-derived sandy soils without a large component of gravel and larger stones, such a two-layer biomantle may not form, or may be very weakly developed and difficult to identify as such. Nonetheless, bioturbation activity by burrowing animals is usually apparent, for example in the form of “krotovina”, in-filled animal burrows.
Besides advocating for a view of soils and their processes with an animal-based, biomantle point of view, these authors spend some time dismissing subaqueous soils (e.g. marine sediments) as simplistic, uncomplicated places lacking many of the key (and very complex) processes that occur in subaerial soils. Their list of such processes near the end of the paper, taken as a kind of justification for their uncited and unsupported dismissal of subaqueous soils, is composed entirely of those processes relating to changing water amounts in terrestrial soils, such as groundwater flow and wetting and drying events. I found their argument unconvincing, as they do not describe any aqueous-only processes such as changes in dissolved-O2 concentrations or the sorting action of water currents, and their blithe disregard for marine biodiversity in statements about how much more diverse the life in terrestrial soils must be, is the proverbial icing on the insult cake. Johnson et al.: please cite some evidence to support such sweeping generalizations.
These authors advocate a new paradigm to underlie studies of soil science and related fields, based on increased recognition of processes occurring in and responsible for the production of the “biomantle”, the upper layer of soil composed of and formed by the actions of organisms. Many of these processes are based on movements of soil and soil components, and so are dominated by animals, especially active burrowers that are responsible for large vertical movements of soil in some environments. The biomantle is defined as being composed of “biofabric”, or materials that owe their existence to the actions of organisms, from the bodies of these organisms themselves, to the materials released by the organisms, to the minerals created by biological processes, to the voids created by their movements and the gases filling those voids released by their metabolisms.
These authors trace their ideas from the writings of Darwin, particularly his final work involving the activity of worms in “vegetable mould”, a late-18th century term for what we now call soil.
A biomantle layer, residing chiefly in the A horizon (or topsoil) can be more easily recognized in some landscapes than others. Humid tropical soils especially may show very thick and distinct biomantles, in two layers. The upper, thicker layer is composed of relatively fine materials, resting on a basal layer of coarser material; this basal layer is referred to here as the stonelayer. Below the stonelayer is non-biomantle, typically a B horizon (or subsoil). The hypothesized process creating this two-layer biomantle is the action of “conveyor belt” animals, especially termites that carry small particles upwards but are unable to move larger stones, thus eventually sorting the soil mineral material.
In other soils, such as loess-derived sandy soils without a large component of gravel and larger stones, such a two-layer biomantle may not form, or may be very weakly developed and difficult to identify as such. Nonetheless, bioturbation activity by burrowing animals is usually apparent, for example in the form of “krotovina”, in-filled animal burrows.
Besides advocating for a view of soils and their processes with an animal-based, biomantle point of view, these authors spend some time dismissing subaqueous soils (e.g. marine sediments) as simplistic, uncomplicated places lacking many of the key (and very complex) processes that occur in subaerial soils. Their list of such processes near the end of the paper, taken as a kind of justification for their uncited and unsupported dismissal of subaqueous soils, is composed entirely of those processes relating to changing water amounts in terrestrial soils, such as groundwater flow and wetting and drying events. I found their argument unconvincing, as they do not describe any aqueous-only processes such as changes in dissolved-O2 concentrations or the sorting action of water currents, and their blithe disregard for marine biodiversity in statements about how much more diverse the life in terrestrial soils must be, is the proverbial icing on the insult cake. Johnson et al.: please cite some evidence to support such sweeping generalizations.
Tuesday, April 20, 2010
Stark and Hart 1996
Stark JM, Hart SC. 1996. Diffusion technique for preparing salt solutions, Kjeldahl digests, and persulfate digests for nitrogen-15 analysis. Soil Science Society of America Journal 60: 1846-1855.
These authors evaluated the recently-developed Teflon-encased-acid-trap technique for collecting nitrogen from water samples for analysis, especially stable isotope (15N) analysis. Earlier acid trap techniques, which rely on the chemistry of ammonium/ammonia in solutions of varying pH, were based on suspended small vials containing acid solutions above a larger volume of sample solution at high pH. Ammonium present in the sample is converted to ammonia by high pH, and escapes solution into the gas phase. It is captured in acid solution; in a closed container with a separate acidic region, ammonium will migrate from the alkaline sample to the acid trap. Suspended trap designs are vulnerable to a number of problems, including vulnerability of the acid trap to contamination by alkaline solution and subsequent loss of captured ammonium. Teflon will pass gases but not liquids, and therefore provides an ideal barrier between the sample and the acid trap that will permit ammonia to enter the trap.
These authors conducted a set of six experiments to evaluate the utility of Teflon acid traps. First, blanks were evaluated, to determine the sensitivity of the technique to nitrogen derived from contamination in the various materials of the experiment (filter paper, Teflon, plastic bottles, etc.). There was some nitrogen detectable from these non-sample sources, but a correction factor could be constructed based on including a few blanks in sample sets. The second experiment examined the recovery of ammonium from 2M KCl solutions. These solutions are very similar to the solutions extracted from soils of Alexandra Fjord in 2009. As might be expected, incubation time correlated with recovery of ammonium; in addition, Teflon traps performed better over shorter incubations (up to about 6 days) than did suspended traps, though the difference disappeared at the longest (8 days) incubations.
The third experiment was of greatest interest to me. They examined the open-bottle time necessary to eliminate residual ammonium from samples used in experiment 2, and the incubation conditions to collect NO3- -derived nitrogen using Devarda’s alloy to reduce NO3- to NH4+. Residual ammonium left in solution at the end of the first reaction would contaminate NO3- examination and lead to overestimation of NO3- contents; this is especially true when the two forms of nitrogen have been previously enriched with 15N to different degrees. There is a trade-off between open bottle time (ranging in these experiments from one to five days) and recovery of NO3- from samples; long open-bottle times appear to lead to an unknown chemical change in samples, which these authors speculate, may involve sorption of atmospheric CO2. Long ammonium-collection times (i.e. experiment 2) do tend to collect the great majority of ammonium present, recovering on average more than 97% of ammonium from known-concentration samples. This suggests to me a long and potentially nitrate-losing open-bottle incubation is not necessary if ammonium collection has proceeded for at least six days. Agitation of samples, in these experiments often once per day, resulted in a strong improvement in nitrogen capture over at least the shorter (24-96 hour) incubations; our use of continuous agitation for seven days therefore seems likely to capture nearly all ammonium present in samples.
Experiments 4 through 6 were of little interest to me, as I am unfamiliar with Kjeldahl digests and persulfate digests and do not plan to use these techniques in my studies. From what I could glean based on my limited knowledge, the Teflon-acid-trap technique appears to work well with Kjeldahl digests and persulfate digests.
Overall, the Teflon-acid-trap technique performed very well, and had significant ease-of-use and contamination-avoiding advantages over earlier methods. One caution put forth by these authors is regarding the H2 gas evolved during Devarda’s alloy incubations; strong build up of gas can cause leaks, potentially allowing NH3 to escape and leading to underestimates of sample nitrate contents. They suggest storing bottles upside-down during such incubations, as leaks will then include sample solution, and leaking bottles can be easily identified.
Complete recovery of nitrogen was not possible on a routine basis using this technique, but 15N isotope ratios do not rely on 100% recovery if ammonium and / or nitrate concentrations have been measured by an independent method, such as the widely-used colorimetric techniques. The two isotopes of nitrogen do not migrate differently between alkaline sample and acid trap, thus even at relatively inefficient recovery rates, isotopic ratios are maintained. Blanks are important, but in general this technique is robust, reliable, and easy to conduct.
These authors evaluated the recently-developed Teflon-encased-acid-trap technique for collecting nitrogen from water samples for analysis, especially stable isotope (15N) analysis. Earlier acid trap techniques, which rely on the chemistry of ammonium/ammonia in solutions of varying pH, were based on suspended small vials containing acid solutions above a larger volume of sample solution at high pH. Ammonium present in the sample is converted to ammonia by high pH, and escapes solution into the gas phase. It is captured in acid solution; in a closed container with a separate acidic region, ammonium will migrate from the alkaline sample to the acid trap. Suspended trap designs are vulnerable to a number of problems, including vulnerability of the acid trap to contamination by alkaline solution and subsequent loss of captured ammonium. Teflon will pass gases but not liquids, and therefore provides an ideal barrier between the sample and the acid trap that will permit ammonia to enter the trap.
These authors conducted a set of six experiments to evaluate the utility of Teflon acid traps. First, blanks were evaluated, to determine the sensitivity of the technique to nitrogen derived from contamination in the various materials of the experiment (filter paper, Teflon, plastic bottles, etc.). There was some nitrogen detectable from these non-sample sources, but a correction factor could be constructed based on including a few blanks in sample sets. The second experiment examined the recovery of ammonium from 2M KCl solutions. These solutions are very similar to the solutions extracted from soils of Alexandra Fjord in 2009. As might be expected, incubation time correlated with recovery of ammonium; in addition, Teflon traps performed better over shorter incubations (up to about 6 days) than did suspended traps, though the difference disappeared at the longest (8 days) incubations.
The third experiment was of greatest interest to me. They examined the open-bottle time necessary to eliminate residual ammonium from samples used in experiment 2, and the incubation conditions to collect NO3- -derived nitrogen using Devarda’s alloy to reduce NO3- to NH4+. Residual ammonium left in solution at the end of the first reaction would contaminate NO3- examination and lead to overestimation of NO3- contents; this is especially true when the two forms of nitrogen have been previously enriched with 15N to different degrees. There is a trade-off between open bottle time (ranging in these experiments from one to five days) and recovery of NO3- from samples; long open-bottle times appear to lead to an unknown chemical change in samples, which these authors speculate, may involve sorption of atmospheric CO2. Long ammonium-collection times (i.e. experiment 2) do tend to collect the great majority of ammonium present, recovering on average more than 97% of ammonium from known-concentration samples. This suggests to me a long and potentially nitrate-losing open-bottle incubation is not necessary if ammonium collection has proceeded for at least six days. Agitation of samples, in these experiments often once per day, resulted in a strong improvement in nitrogen capture over at least the shorter (24-96 hour) incubations; our use of continuous agitation for seven days therefore seems likely to capture nearly all ammonium present in samples.
Experiments 4 through 6 were of little interest to me, as I am unfamiliar with Kjeldahl digests and persulfate digests and do not plan to use these techniques in my studies. From what I could glean based on my limited knowledge, the Teflon-acid-trap technique appears to work well with Kjeldahl digests and persulfate digests.
Overall, the Teflon-acid-trap technique performed very well, and had significant ease-of-use and contamination-avoiding advantages over earlier methods. One caution put forth by these authors is regarding the H2 gas evolved during Devarda’s alloy incubations; strong build up of gas can cause leaks, potentially allowing NH3 to escape and leading to underestimates of sample nitrate contents. They suggest storing bottles upside-down during such incubations, as leaks will then include sample solution, and leaking bottles can be easily identified.
Complete recovery of nitrogen was not possible on a routine basis using this technique, but 15N isotope ratios do not rely on 100% recovery if ammonium and / or nitrate concentrations have been measured by an independent method, such as the widely-used colorimetric techniques. The two isotopes of nitrogen do not migrate differently between alkaline sample and acid trap, thus even at relatively inefficient recovery rates, isotopic ratios are maintained. Blanks are important, but in general this technique is robust, reliable, and easy to conduct.
Thursday, April 15, 2010
Palmer et al. 2010
Palmer K, Drake HL, Horn MA. 2010. Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Applied and Enironmental Microbiology 76: 1125-1134.
These authors examined soils from an acidic fen in southern Germany, and discovered novel denitrifiers that are apparently adapted to local conditions and contribute to the cycling of nitrogen within the fen. Methods employed included measurement of soil parameters, microcosms to examine denitrification rates (both total denitrification and net production / consumption of N2O), cell counts of cultured organisms, and phylogenetic analysis using narG and nosZ sequences and RFLP.
These authors examined soils from an acidic fen in southern Germany, and discovered novel denitrifiers that are apparently adapted to local conditions and contribute to the cycling of nitrogen within the fen. Methods employed included measurement of soil parameters, microcosms to examine denitrification rates (both total denitrification and net production / consumption of N2O), cell counts of cultured organisms, and phylogenetic analysis using narG and nosZ sequences and RFLP.
Tuesday, April 6, 2010
Palmer et al. 2009
Palmer K, Drake HL, Horn MA. 2009. Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers. Applied and Environmental Microbiology 75: 5170-5174.
These authors compared the sequences of narG and nosZ genes to corresponding sequences of 16s rRNA genes, using in-silico analysis of sequences downloaded from GenBank. While similarities above 97% are commonly used for species- or genus-level taxonomic delineation for 16s sequences, this analysis found much lower threshold similarities for such delineation using the structural genes.
This paper is confusing to me. One part of the text appears to contradict itself, when the authors state that the Nar operon in Pseudomonas stutzeri A1501 is putatively alien in origin (i.e. recent horizontal transfer), then go on to state in the same paragraph that it appears unlikely that the Nar operon was horizontally transferred in any species. I may just be misunderstanding the meaning of the term “putatively alien” in regards to a bacterial gene sequence.
A greater puzzle is presented by the list of nosZ sequences. These authors downloaded 85 such sequences, where my own attempts to extract data from GenBank resulted in only 42 unique nosZ sequences. The list in a supplementary table includes several cases of multiple accessions of the same species but of different PD. The paper these clusters of PD-sequences are derived from is Dandie et al. (2007); a quick scan of this paper did not reveal what the distinction “PD” indicates.
These authors compared the sequences of narG and nosZ genes to corresponding sequences of 16s rRNA genes, using in-silico analysis of sequences downloaded from GenBank. While similarities above 97% are commonly used for species- or genus-level taxonomic delineation for 16s sequences, this analysis found much lower threshold similarities for such delineation using the structural genes.
This paper is confusing to me. One part of the text appears to contradict itself, when the authors state that the Nar operon in Pseudomonas stutzeri A1501 is putatively alien in origin (i.e. recent horizontal transfer), then go on to state in the same paragraph that it appears unlikely that the Nar operon was horizontally transferred in any species. I may just be misunderstanding the meaning of the term “putatively alien” in regards to a bacterial gene sequence.
A greater puzzle is presented by the list of nosZ sequences. These authors downloaded 85 such sequences, where my own attempts to extract data from GenBank resulted in only 42 unique nosZ sequences. The list in a supplementary table includes several cases of multiple accessions of the same species but of different PD. The paper these clusters of PD-sequences are derived from is Dandie et al. (2007); a quick scan of this paper did not reveal what the distinction “PD” indicates.
Thursday, April 1, 2010
Tuomivirta et al. 2009
Tuomivirta TT, Yrjälä K, Frize H. 2009. Quantitative PCR of pmoA using a novel reverse primer correlates with potential methane oxidation in Finnish Fen. Research in Microbiology 160: 751-756.
These authors developed novel primers for studying the methanotrophs of Finnish peatland fens. The existing primer pairs widely used to study methanotrophs, based on the gene pmoA, did not consistently amplify useful products in PCR using template DNA from these fens.
The novel primer pair was tested on 114 samples from two Finnish fens, representing the northern and southern peatlands of Finland. While A189f/A682r failed to provide useful products, the new primer A6821r in conjunction with A189f did produce strong bands. In qPCR, these primers produced results correlated with measured methane oxidation potential, further supporting their utility in these systems.
These authors developed novel primers for studying the methanotrophs of Finnish peatland fens. The existing primer pairs widely used to study methanotrophs, based on the gene pmoA, did not consistently amplify useful products in PCR using template DNA from these fens.
The novel primer pair was tested on 114 samples from two Finnish fens, representing the northern and southern peatlands of Finland. While A189f/A682r failed to provide useful products, the new primer A6821r in conjunction with A189f did produce strong bands. In qPCR, these primers produced results correlated with measured methane oxidation potential, further supporting their utility in these systems.
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