Delgado JA, Del Grosso SJ, Ogle SM. 2010. 15N isotopic crop residue cycling studies and modeling suggest that IPCC methodologies to assess residue contributions to N2O-N emissions should be reevaluated. Nutrient Cycling in Agroecosystems 86: 383-390.
These authors reanalyzed two recent reviews of measuring nitrous oxide emissions from agricultural systems and used a model to simulate N2O emissions and NO3 leaching associated with cropping practices in Colorado and Iowa. In general, use of crop residue instead of or in addition to synthetic fertilizers significantly altered patterns of N loss, whereas IPCC recommendations assume no difference between these N sources in regards to N2O emissions. Microbial immobilization of nitrogen, particularly associated with residues with high C/N ratios, is a major factor in these differences, and these authors provide supporting arguments for their suggestion of revisions to IPCC recommendations and modeling.
Showing posts with label Climate. Show all posts
Showing posts with label Climate. Show all posts
Wednesday, September 29, 2010
Monday, September 27, 2010
Smith et al. 2003
Smith KA, Ball T, Conen F, Dobbie KE, Massheder J, Rey A. 2003. Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. European Journal of Soil Science 54:779-791.
These authors present a broad review paper of the role of soil physical factors, mainly temperature and water-filled-pore-space, in controlling soil emissions of the greenhouse gases CO2, CH4, and N2O. The paper’s goal is stated to be to expose a variety of researchers to the links between soil physics and soil biology, as well as the importance of these fields to current research in many disciplines on global warming.
All three gases are produced and consumed in soil primarily by microorganisms, which respond to variation in soil physical parameters in different ways. In general, both temperature and WFPS impact GHG production. Higher temperatures almost always result in increased production of gases, though the Q10 values (measuring the magnitude of response to a change of 10º of temperature) vary widely in the literature for all three gases. The effect of WFPS is different, involving upper and lower bounds, though in the middle range increasing WFPS generally promotes increased gas production. Microbes are limited in their tolerance of dry conditions, such that gas production falls rapidly below some critical WFPS value; for CO2 this threshold is near 20%. WFPS is also indirectly important, through its effects on soil diffusivity. Higher WFPS as well as higher bulk density are associated with lessened CH4 oxidation, due to reduced diffusivity of both CH4 and atmospheric O2. Very high WFPS values are associated with reduction of N2O to N2, partly by limiting O2 supplies and creating larger anaerobic microsites, and partly by preventing the escape of N2O gas into rapid-diffusion pathways; it is trapped in the vicinity of microbes capable of using it as an electron acceptor.
There are other factors controlling net GHG emissions, such as the relationship between plant productivity and water table position, which will change the relationship between rates of soil organic matter oxidation to CO2 and the removal of CO2 from the atmosphere by plants; trees in particular can lower local water tables, increasing SOM oxidation while simultaneously consuming more CO2 than the previous wetland vegetation community.
I read this paper on the suggestion of my coworkers in the special topics class of fall 2010, but it applies well to the general area of my research. The reference list includes multiple interesting papers addressing particular specialties within this large topic.
These authors present a broad review paper of the role of soil physical factors, mainly temperature and water-filled-pore-space, in controlling soil emissions of the greenhouse gases CO2, CH4, and N2O. The paper’s goal is stated to be to expose a variety of researchers to the links between soil physics and soil biology, as well as the importance of these fields to current research in many disciplines on global warming.
All three gases are produced and consumed in soil primarily by microorganisms, which respond to variation in soil physical parameters in different ways. In general, both temperature and WFPS impact GHG production. Higher temperatures almost always result in increased production of gases, though the Q10 values (measuring the magnitude of response to a change of 10º of temperature) vary widely in the literature for all three gases. The effect of WFPS is different, involving upper and lower bounds, though in the middle range increasing WFPS generally promotes increased gas production. Microbes are limited in their tolerance of dry conditions, such that gas production falls rapidly below some critical WFPS value; for CO2 this threshold is near 20%. WFPS is also indirectly important, through its effects on soil diffusivity. Higher WFPS as well as higher bulk density are associated with lessened CH4 oxidation, due to reduced diffusivity of both CH4 and atmospheric O2. Very high WFPS values are associated with reduction of N2O to N2, partly by limiting O2 supplies and creating larger anaerobic microsites, and partly by preventing the escape of N2O gas into rapid-diffusion pathways; it is trapped in the vicinity of microbes capable of using it as an electron acceptor.
There are other factors controlling net GHG emissions, such as the relationship between plant productivity and water table position, which will change the relationship between rates of soil organic matter oxidation to CO2 and the removal of CO2 from the atmosphere by plants; trees in particular can lower local water tables, increasing SOM oxidation while simultaneously consuming more CO2 than the previous wetland vegetation community.
I read this paper on the suggestion of my coworkers in the special topics class of fall 2010, but it applies well to the general area of my research. The reference list includes multiple interesting papers addressing particular specialties within this large topic.
Thursday, August 19, 2010
Christiansen 1979
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.
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, 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.
Thursday, March 25, 2010
Harding et al. 2001
Harding RJ, Gryning S-E, Halldin S, Lloyd CR. 2001. Progress in understanding of land surface/atmosphere exchanges at high latitudes. Theoretical and Applied Climatology 70: 5-18.
These authors review and discuss the implications of studies based in two international projects in northern Europe. WINTEX was a large study examining the effects of snow cover and long nights in winter on high-latitude ground-atmosphere exchange processes, while LAPP was an independent but complementary study examining most of the same processes in a range of high latitude sites during spring and summer.
Snow cover plays a major role in Arctic exchange processes. The high albedo of snow reflects much of the incident solar radiation, and insulates the frozen ground below, prolonging the period of snow cover to upwards of 9 months in the year in many places. Where vegetation is tall, such as in the boreal forest, the low solar angle reduces the effective net albedo of the landscape, allowing sunlight to warm the dark trees and speed springtime melting. This study mentions the importance of snow-surface aerodynamics, though it appears there is little solid information on this complex topic.
Snow melt is the major hydrological event of the year in much of the Arctic. The combination of frozen soils, very low evaporation rates, and often flat terrain means much of the Arctic is very wet or saturated while annual precipitation rates are consistent with arid or semi-arid conditions. These areas are the classic tundra systems, with abundant shallow lakes and ponds and very wet high-organic soils.
Differences in snow-surface dynamics and the timing of snowmelt create an extremely heterogeneous landscape, particularly in the vicinity of the northern treeline. There are often very large temperature and air-flow differences between patches of trees and adjacent lakes or clearings, which greatly complicate attempts to model the carbon dioxide emissions (for example) of such areas. Much of this paper is a series of evaluations of some of the models that have been applied to this region. In general, more sophisticated models that can take some of the extreme variability into account perform better than models that cannot account for differences in snow depth or insulating properties. However, this paper makes it clear that current modelling efforts still leave much to be desired in terms of predicting Arctic heat budgets and biological responses.
Water storage is also very difficult to model, and has large and variable impacts on other parts of the system. There appears to be large and unpredictable year-to-year variation in water storage and transport at the scale of catchments and basins, and the importance of soil water in controlling biological processes such as the decomposition of organic matter is large. Runoff matters, even on very gentle slopes.
This paper provides a useful overview of large-scale processes and attempts to understand these processes in the Arctic.
These authors review and discuss the implications of studies based in two international projects in northern Europe. WINTEX was a large study examining the effects of snow cover and long nights in winter on high-latitude ground-atmosphere exchange processes, while LAPP was an independent but complementary study examining most of the same processes in a range of high latitude sites during spring and summer.
Snow cover plays a major role in Arctic exchange processes. The high albedo of snow reflects much of the incident solar radiation, and insulates the frozen ground below, prolonging the period of snow cover to upwards of 9 months in the year in many places. Where vegetation is tall, such as in the boreal forest, the low solar angle reduces the effective net albedo of the landscape, allowing sunlight to warm the dark trees and speed springtime melting. This study mentions the importance of snow-surface aerodynamics, though it appears there is little solid information on this complex topic.
Snow melt is the major hydrological event of the year in much of the Arctic. The combination of frozen soils, very low evaporation rates, and often flat terrain means much of the Arctic is very wet or saturated while annual precipitation rates are consistent with arid or semi-arid conditions. These areas are the classic tundra systems, with abundant shallow lakes and ponds and very wet high-organic soils.
Differences in snow-surface dynamics and the timing of snowmelt create an extremely heterogeneous landscape, particularly in the vicinity of the northern treeline. There are often very large temperature and air-flow differences between patches of trees and adjacent lakes or clearings, which greatly complicate attempts to model the carbon dioxide emissions (for example) of such areas. Much of this paper is a series of evaluations of some of the models that have been applied to this region. In general, more sophisticated models that can take some of the extreme variability into account perform better than models that cannot account for differences in snow depth or insulating properties. However, this paper makes it clear that current modelling efforts still leave much to be desired in terms of predicting Arctic heat budgets and biological responses.
Water storage is also very difficult to model, and has large and variable impacts on other parts of the system. There appears to be large and unpredictable year-to-year variation in water storage and transport at the scale of catchments and basins, and the importance of soil water in controlling biological processes such as the decomposition of organic matter is large. Runoff matters, even on very gentle slopes.
This paper provides a useful overview of large-scale processes and attempts to understand these processes in the Arctic.
Saturday, January 9, 2010
Wagner et al. 2009
Wagner D, Kobabe S, Liebner S. 2009. Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia. Canadian Journal of Microbiology 55: 73-83.
These authors examined the microbial communities at two depth bands (near-surface and near-permafrost) in low-centred tundra polygons at the vast permafrost wetland of the delta of the Lena River. The delta covers more than 60 000 km^2, and much of it appears to be a reserve or national park of Russia. The CAVM (Walker et al. 2002) describes most of the delta as vegetation type W2, sedge, moss, dwarf-shrub wetland, and satellite images from Google maps shows very extensive lake and pond coverage of the landscape. In short, it’s pretty wet, and generally cold.
The general finding of this paper is that while near-surface communities include a wide diversity of aerobic and facultatively-anaerobic bacteria, the deeper, colder, anaerobic portions of the soil contain almost no aerobes, and are instead dominated by “fermenting” species capable of decomposing recalcitrant organic carbon molecules under negative-redox conditions. There is a sharp temperature gradient, which combined with the poorer quality of carbon, the lack of oxygen and negative redox conditions, and the general water saturation at depth creates conditions near the permafrost suitable only for the slow microbial metabolisms. None of this is particularly surprising, but the observation of decreased biodiversity with water saturation does suggest the worrying possibility that increased water in this system, driven by melting permafrost and climate change (particularly upstream in the long and North-flowing Lena) could drive these microbial communities to lose some “physiological skills” such as the ability to oxidize methane, a metabolic pathway possessed only by some aerobic prokaryotes.
This paper is quite important to my own work, I think. Besides emphasizing the role of water content in structuring soil chemical and especially biological conditions, the description of the methods used to measure microbial biodiversity should be useful. However, while the BIOLOG plates seem interesting, the results of this technique are not at all well explained in this paper. I do not know what is indicated by the relationship shown in Figure 3, for example, of changes in colour development associated with carbon turnover of various categories of organic substrates. Several of the figures are simple plots of principal component analysis (PCA), literally just PC1 vs. PC2 with some outlines drawn around some clusters. I’m sure there is more of interest in this paper besides the coarse outline of biodiversity differences in communities, but without a more thorough explanation of the nearly-raw data I cannot see it.
These authors examined the microbial communities at two depth bands (near-surface and near-permafrost) in low-centred tundra polygons at the vast permafrost wetland of the delta of the Lena River. The delta covers more than 60 000 km^2, and much of it appears to be a reserve or national park of Russia. The CAVM (Walker et al. 2002) describes most of the delta as vegetation type W2, sedge, moss, dwarf-shrub wetland, and satellite images from Google maps shows very extensive lake and pond coverage of the landscape. In short, it’s pretty wet, and generally cold.
The general finding of this paper is that while near-surface communities include a wide diversity of aerobic and facultatively-anaerobic bacteria, the deeper, colder, anaerobic portions of the soil contain almost no aerobes, and are instead dominated by “fermenting” species capable of decomposing recalcitrant organic carbon molecules under negative-redox conditions. There is a sharp temperature gradient, which combined with the poorer quality of carbon, the lack of oxygen and negative redox conditions, and the general water saturation at depth creates conditions near the permafrost suitable only for the slow microbial metabolisms. None of this is particularly surprising, but the observation of decreased biodiversity with water saturation does suggest the worrying possibility that increased water in this system, driven by melting permafrost and climate change (particularly upstream in the long and North-flowing Lena) could drive these microbial communities to lose some “physiological skills” such as the ability to oxidize methane, a metabolic pathway possessed only by some aerobic prokaryotes.
This paper is quite important to my own work, I think. Besides emphasizing the role of water content in structuring soil chemical and especially biological conditions, the description of the methods used to measure microbial biodiversity should be useful. However, while the BIOLOG plates seem interesting, the results of this technique are not at all well explained in this paper. I do not know what is indicated by the relationship shown in Figure 3, for example, of changes in colour development associated with carbon turnover of various categories of organic substrates. Several of the figures are simple plots of principal component analysis (PCA), literally just PC1 vs. PC2 with some outlines drawn around some clusters. I’m sure there is more of interest in this paper besides the coarse outline of biodiversity differences in communities, but without a more thorough explanation of the nearly-raw data I cannot see it.
Thursday, November 26, 2009
Angel and Conrad 2009
Angel RA, Conrad R. 2009. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environmental Microbiology 11: 2598-2610.
These authors examined the methanotroph communities of sub-tropical desert soils in Israel, using both field and lab measurements of methane fluxes and molecular investigation of sampled microbes. Negative surface flux, indicating consumption of atmospheric methane by soil, was found only at an undisturbed site in this study; the 4 other sites were varying degrees of agricultural and did not show clear patterns of consumption of methane at low concentrations. Addition of water, simulating a typical local rainfall event, eliminated methanotroph activity for about 12 hours, then this activity rebounded to well above background for up to 48 hours. This process of apparent short-term community dynamics was not investigated or discussed in much detail by these authors, though I found it one of the most interesting observations.
Methanotrophs were identified in soil samples by the usual suite of molecular biology methods. One set of primers used here is described as also targeting certain clades of amoA, a gene prominent in ammonia oxidation. These primers were successful at amplifying sequences even from soils in which methanotrophic activity had not been detected, suggesting that many or all of the sequences amplified by these primers were not actually methanotroph sequences, but rather sequences from apparently ubiquitous ammonia oxidizing bacteria.
The target gene for methanotrophs encodes a membrane-bound protein involved in transporting methane into the cytoplasm. From the way some primers also targeted amoA, I think perhaps there is a shared ancestry among the pathways for scavenging environmental ammonia and for scavenging environmental methane, though these authors do not delve into that discussion.
This paper was apparently instrumental in structuring the thoughts of my co-author (Dr. Siciliano) regarding how we should structure the manuscripts we are preparing based on the 2009 Alexandra Fjord field season. Up to this paper, we had been considering including both molecular analysis (based mainly on qPCR) and soil-properties (nutrients, root exudates, moisture, trace gases, etc.) in our nascent “Pits & Probes” manuscript. However, this paper demonstrates the considerable volume of work required to achieve a useful molecular dataset, suggesting that we would be better off saving these DNA data for a subsequent study, where they can be described and analyzed at the appropriate level of detail.
These authors examined the methanotroph communities of sub-tropical desert soils in Israel, using both field and lab measurements of methane fluxes and molecular investigation of sampled microbes. Negative surface flux, indicating consumption of atmospheric methane by soil, was found only at an undisturbed site in this study; the 4 other sites were varying degrees of agricultural and did not show clear patterns of consumption of methane at low concentrations. Addition of water, simulating a typical local rainfall event, eliminated methanotroph activity for about 12 hours, then this activity rebounded to well above background for up to 48 hours. This process of apparent short-term community dynamics was not investigated or discussed in much detail by these authors, though I found it one of the most interesting observations.
Methanotrophs were identified in soil samples by the usual suite of molecular biology methods. One set of primers used here is described as also targeting certain clades of amoA, a gene prominent in ammonia oxidation. These primers were successful at amplifying sequences even from soils in which methanotrophic activity had not been detected, suggesting that many or all of the sequences amplified by these primers were not actually methanotroph sequences, but rather sequences from apparently ubiquitous ammonia oxidizing bacteria.
The target gene for methanotrophs encodes a membrane-bound protein involved in transporting methane into the cytoplasm. From the way some primers also targeted amoA, I think perhaps there is a shared ancestry among the pathways for scavenging environmental ammonia and for scavenging environmental methane, though these authors do not delve into that discussion.
This paper was apparently instrumental in structuring the thoughts of my co-author (Dr. Siciliano) regarding how we should structure the manuscripts we are preparing based on the 2009 Alexandra Fjord field season. Up to this paper, we had been considering including both molecular analysis (based mainly on qPCR) and soil-properties (nutrients, root exudates, moisture, trace gases, etc.) in our nascent “Pits & Probes” manuscript. However, this paper demonstrates the considerable volume of work required to achieve a useful molecular dataset, suggesting that we would be better off saving these DNA data for a subsequent study, where they can be described and analyzed at the appropriate level of detail.
Thursday, November 12, 2009
Wrage et al. 2004
Wrage N, Lauf J, del Prado A, Pinto M, Pietrzak S, Yamulki S, Oenema O, Gebauer G. 2004. Distinguishing sources of N2O in European grasslands by stable isotope analysis. Rapid Communications in Mass Spectrometry 18: 1201-1207.
These authors used the signature ratios of stable isotopes of oxygen and nitrogen in a range of soil chemicals and microbial metabolic pathways to identify the source of N2O produced in grasslands monitored as part of a long-term greenhouse gas international experiment. There are 3 known pathways to N2O production: nitrification, in which N2O is produced as a by-product of ammonium oxidation to nitrate, nitrifier denitrification, in which nitrifying organisms reduce nitrite to dinitrogen gas via N2O, especially under anaerobic conditions, and denitrification, in which nitrate is reduced to dinitrogen gas via N2O by denitrifying organisms.
Previous studies had often used acetylene to inhibit N2O production, but this has been found to be unreliable. In contrast, the stable isotope approach used here was able to detect both N2O production and consumption even when reservoirs of N2O were very low. Nitrification was the most important N-transforming process found in these systems, with most N2O produced probably from reduction pathways.
These authors used the signature ratios of stable isotopes of oxygen and nitrogen in a range of soil chemicals and microbial metabolic pathways to identify the source of N2O produced in grasslands monitored as part of a long-term greenhouse gas international experiment. There are 3 known pathways to N2O production: nitrification, in which N2O is produced as a by-product of ammonium oxidation to nitrate, nitrifier denitrification, in which nitrifying organisms reduce nitrite to dinitrogen gas via N2O, especially under anaerobic conditions, and denitrification, in which nitrate is reduced to dinitrogen gas via N2O by denitrifying organisms.
Previous studies had often used acetylene to inhibit N2O production, but this has been found to be unreliable. In contrast, the stable isotope approach used here was able to detect both N2O production and consumption even when reservoirs of N2O were very low. Nitrification was the most important N-transforming process found in these systems, with most N2O produced probably from reduction pathways.
Friday, November 6, 2009
Elberling et al. 2004
Elberling B, Jakobsen BH, Berg P, Sondergaard J, Sigsgaard C. 2004. Influence of vegetation, temperature, and water content on soil carbon distribution and mineralization in four High Arctic soils. Arctic, Antarctic, and Alpine Research, 36: 528-538.
These authors examined the carbon pools and carbon dioxide effluxes from four ecosystems at Zackenberg, in north-east Greenland. Their four ecosystems are very similar to the Alexandra Fjord systems of Dryas (CAVM P1), Cassiope (P2), Salix (G3), and Wet Sedge Meadow (W1).
There are two major sources of soil CO2: respiration by plant roots, and microbial respiration. Which of these two processes dominates CO2 production is a matter of some debate, with studies in the 1990s and 2000s indicating either when measuring similar arctic ecosystems. This study does not settle that debate, with estimated ratios of the two processes ranging from 9:1 to 1:9. What is clear is that plants and microbes compete for resources in arctic soils, with considerable variation in both time and space, even among vegetation communities in one valley with a consistent above-ground climate.
These soils include a buried A-horizon, with birch leaves present in pockets of organic-rich former topsoil indicative of surface conditions during the previous climatic mild period approximately 5000 years ago. These pockets of “Ab” create something of a wildcard situation for CO2 evolution, being responsible for a considerable fraction of the measured CO2 efflux at all ecosystems to varying extent.
To measure subsurface concentrations of CO2, these authors extended a probe to a range of depths and connected it to their gas analyzer also used for measuring surface fluxes, much as we have done at Alexandra Fjord. However, their gas analyzer only measures CO2, and they did not allow their probes to equilibrate to subsurface conditions for very long; a few minutes seems to be the usual protocol in this case.
A range of soil parameters were measured, and in general variation between vegetation types in these parameters exceeded variation within. The Cassiope system was the most variable, but also had the most variable Ab layers, which probably accounted for most of the variation. These patterns of variation at all ecosystems, however, suggest that the effects of climate change will not be uniform across the High Arctic, with increased temperatures leading to perhaps increases or decreases in the decomposition of buried organic matter and CO2 effluxes.
Like our own results from Alexandra Fjord, the Salix ecosystem at Zackenberg showed the highest below-ground CO2 concentrations. At Zackenberg, CO2 concentrations in Salix were mostly related to microbial decomposition of organic matter, with reduced soil water content leading to more oxygenation and higher temperatures, both increasing the rate of decomposition. In contrast, the water-saturated Eriophorum system had very high carbon stores and the highest CO2 efflux, but a decrease in water levels here leads to a shift from methane production to CO2 production, rather than a simple increase in one rate.
Overall, this paper provides some results and considerations of high relevance to my own work, especially given the high overlap in the range of ecosystems under consideration and the range of methods employed in their analysis. Their systems are not identical to those I studied; for example, the Dryas system at Zackenberg appears to be considerably drier and with less vegetation cover compared to the system with the same name at Alexandra Fjord.
These authors examined the carbon pools and carbon dioxide effluxes from four ecosystems at Zackenberg, in north-east Greenland. Their four ecosystems are very similar to the Alexandra Fjord systems of Dryas (CAVM P1), Cassiope (P2), Salix (G3), and Wet Sedge Meadow (W1).
There are two major sources of soil CO2: respiration by plant roots, and microbial respiration. Which of these two processes dominates CO2 production is a matter of some debate, with studies in the 1990s and 2000s indicating either when measuring similar arctic ecosystems. This study does not settle that debate, with estimated ratios of the two processes ranging from 9:1 to 1:9. What is clear is that plants and microbes compete for resources in arctic soils, with considerable variation in both time and space, even among vegetation communities in one valley with a consistent above-ground climate.
These soils include a buried A-horizon, with birch leaves present in pockets of organic-rich former topsoil indicative of surface conditions during the previous climatic mild period approximately 5000 years ago. These pockets of “Ab” create something of a wildcard situation for CO2 evolution, being responsible for a considerable fraction of the measured CO2 efflux at all ecosystems to varying extent.
To measure subsurface concentrations of CO2, these authors extended a probe to a range of depths and connected it to their gas analyzer also used for measuring surface fluxes, much as we have done at Alexandra Fjord. However, their gas analyzer only measures CO2, and they did not allow their probes to equilibrate to subsurface conditions for very long; a few minutes seems to be the usual protocol in this case.
A range of soil parameters were measured, and in general variation between vegetation types in these parameters exceeded variation within. The Cassiope system was the most variable, but also had the most variable Ab layers, which probably accounted for most of the variation. These patterns of variation at all ecosystems, however, suggest that the effects of climate change will not be uniform across the High Arctic, with increased temperatures leading to perhaps increases or decreases in the decomposition of buried organic matter and CO2 effluxes.
Like our own results from Alexandra Fjord, the Salix ecosystem at Zackenberg showed the highest below-ground CO2 concentrations. At Zackenberg, CO2 concentrations in Salix were mostly related to microbial decomposition of organic matter, with reduced soil water content leading to more oxygenation and higher temperatures, both increasing the rate of decomposition. In contrast, the water-saturated Eriophorum system had very high carbon stores and the highest CO2 efflux, but a decrease in water levels here leads to a shift from methane production to CO2 production, rather than a simple increase in one rate.
Overall, this paper provides some results and considerations of high relevance to my own work, especially given the high overlap in the range of ecosystems under consideration and the range of methods employed in their analysis. Their systems are not identical to those I studied; for example, the Dryas system at Zackenberg appears to be considerably drier and with less vegetation cover compared to the system with the same name at Alexandra Fjord.
Friday, October 9, 2009
Nemergut et al. 2005
Nemergut DR, Costello EK, Meyer AF, Pescador MY, Weintraub MN, Schmidt SK. 2005. Structure and function of alpine and arctic soil microbial communities. Research in Microbiology 156: 775-784.
These authors review the current state of knowledge of microbial communities in cold- and snow-affected soils. Their primary study site is a ridge in Colorado with a range of habitats from sub-alpine forest to glaciated mountain-tops; all areas receive significant snow cover for much of the year. They describe only three studies of microbial communities in the Arctic, stating these are the only such studies to their knowledge at the time of preparation of this paper.
The referenced work in this review clearly demonstrates that microbial communities are active when snow covered, contrary to the previous assumption that low temperatures would effectively prohibit microbial metabolisms during winter. Indeed, microbial biomass is actually highest in winter in the alpine tundra systems studied and lowest in spring after an apparent population crash. A wide diversity of microbes has been found, from Bacteria, Archaea, and Eucaryea, including deeply divergent lineages with no known associations with described groups. The physiologies and ecological functions of many of these microbes are completely unknown.
This paper provides a useful overview of the state of the field of cold-soils microecology, with many interesting references and some surprising synthesized findings. This research group in Colorado appears to be one of the few groups in the world studying cold soil microbial communities and their links to climate change.
These authors review the current state of knowledge of microbial communities in cold- and snow-affected soils. Their primary study site is a ridge in Colorado with a range of habitats from sub-alpine forest to glaciated mountain-tops; all areas receive significant snow cover for much of the year. They describe only three studies of microbial communities in the Arctic, stating these are the only such studies to their knowledge at the time of preparation of this paper.
The referenced work in this review clearly demonstrates that microbial communities are active when snow covered, contrary to the previous assumption that low temperatures would effectively prohibit microbial metabolisms during winter. Indeed, microbial biomass is actually highest in winter in the alpine tundra systems studied and lowest in spring after an apparent population crash. A wide diversity of microbes has been found, from Bacteria, Archaea, and Eucaryea, including deeply divergent lineages with no known associations with described groups. The physiologies and ecological functions of many of these microbes are completely unknown.
This paper provides a useful overview of the state of the field of cold-soils microecology, with many interesting references and some surprising synthesized findings. This research group in Colorado appears to be one of the few groups in the world studying cold soil microbial communities and their links to climate change.
Thursday, October 8, 2009
Lipson et al. 2009
Lipson DA, Monson RK, Schmidt SK, Weintraub MN. 2009. The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest. Biogeochemistry 95: 23-35.
These authors conducted a multiply-combined approach study that examined soil microbial communities in the sub-alpine forest of Colorado. They investigated growth and respiration of microbes including both bacteria and fungi, how those processes varied between summer (snow free) and winter (snow covered), and linked these processes to measures of community composition, and built a mathematical model of soil microbial metabolism and temperature. The overall purpose of this study was to thoroughly examine soil microbial processes relating to CO2 emissions and carbon cycling.
The major finding of this study was that there are effectively two distinct microbial communities in this ecosystem. In summer, there is a community of slow-growing, high biomass-yield microbes with a low specific respiration; in other words, the summer microbes grow slowly but efficiently, capturing much of the available carbon as biomass and releasing relatively little CO2 per unit biomass. In winter, the community is composed of fast-growing, low yield microbes that release much more CO2 per unit biomass.
There are effectively two ecological strategies at work, during different seasons. The winter strategy is one of competition. Available nutrients are consumed rapidly, releasing large amounts of CO2 but producing little growth. In summer, the strategy is more cooperative, with slower, less scramble-like growth that more fully uses available nutrients in growing new cells.
In general, the bacteria in the system seem more capable of the high-competition strategy, as these authors found little contribution of fungi to total ecosystem respiration in winter, by using a set of bacterial and fungal inhibitors. The winter community has a much higher response to temperature (Q10) than the summer community. A winter community at intermediate temperatures produces much more CO2 than does a summer community.
In analyzing the composition of the communities, these authors employed the P-test method of Martin (2002), as I intend to as well. I found this paper through a Web of Science search for papers citing Martin (2002); this was one of 153 papers found. The first author of this paper, D.A. Lipson, appears to have a substantial history of publications examining soil microbial communities.
These authors conducted a multiply-combined approach study that examined soil microbial communities in the sub-alpine forest of Colorado. They investigated growth and respiration of microbes including both bacteria and fungi, how those processes varied between summer (snow free) and winter (snow covered), and linked these processes to measures of community composition, and built a mathematical model of soil microbial metabolism and temperature. The overall purpose of this study was to thoroughly examine soil microbial processes relating to CO2 emissions and carbon cycling.
The major finding of this study was that there are effectively two distinct microbial communities in this ecosystem. In summer, there is a community of slow-growing, high biomass-yield microbes with a low specific respiration; in other words, the summer microbes grow slowly but efficiently, capturing much of the available carbon as biomass and releasing relatively little CO2 per unit biomass. In winter, the community is composed of fast-growing, low yield microbes that release much more CO2 per unit biomass.
There are effectively two ecological strategies at work, during different seasons. The winter strategy is one of competition. Available nutrients are consumed rapidly, releasing large amounts of CO2 but producing little growth. In summer, the strategy is more cooperative, with slower, less scramble-like growth that more fully uses available nutrients in growing new cells.
In general, the bacteria in the system seem more capable of the high-competition strategy, as these authors found little contribution of fungi to total ecosystem respiration in winter, by using a set of bacterial and fungal inhibitors. The winter community has a much higher response to temperature (Q10) than the summer community. A winter community at intermediate temperatures produces much more CO2 than does a summer community.
In analyzing the composition of the communities, these authors employed the P-test method of Martin (2002), as I intend to as well. I found this paper through a Web of Science search for papers citing Martin (2002); this was one of 153 papers found. The first author of this paper, D.A. Lipson, appears to have a substantial history of publications examining soil microbial communities.
Wednesday, September 23, 2009
Freeman et al. 2009
Freeman KR, Pescador MY, Reed SC, Costello EK, Robeson MS, Schmidt SK. 2009. Soil CO2 flux and photoautotrophic community composition in high-elevation, ‘barren’ soil. Environmental Microbiology 11: 674-686.
These authors measured photosynthetic carbon fixation and microbial community composition in sub-nival barren soils in the Colorado Front Range of the United States, at 40ºN latitude and approximately 3600m altitude. Like polar desert soils, these sub-nival soils lack conspicuous macrophytic vegetation (vascular plants and bryophytes) and are snow-covered for most of the year. Previous examinations of these systems had suggested the majority of carbon input to these soils was derived from wind-blown dust, but this study demonstrated a much larger input of carbon from in-situ photosynthesis.
Net carbon fixation was estimated by subtracting in-light measurements from in-dark measurements of CO2 flux. All measurements were made using an IRGA system with a 1.18L transparent chamber; dark measurements were made by covering the chamber with a dark, opaque cloth. After measurement of CO2 flux, one site was carefully dug up and transported to the laboratory for molecular-phylogenetic analysis.
The soil was divided into 2 depths: 0-2cm and 2-4cm, then DNA was extracted and PCR using universal bacterial primers for the 16s region was carried out, followed by sequencing. This generated more than 1000 sequences, in 4 bacterial divisions containing known photoautotrophic microorganisms, plus some sequences from eukaryotic green algae.
The most intriguing group of bacteria found were the Chloroflexi, an understudied group found in both depth layers. The taxa composition found in the deeper layer was highly different from the community found in the surface, light-receiving zone, and the authors suggest, based on a few studies done of Chloroflexi in hot-springs environments, that this group may use longer-wavelength light which penetrates deeper in soils. These authors do not make it, but this suggests to me the microphotoautotrophs in this system may be partitioning their environment in both space (depth) and spectrum (red).
This paper includes a large number of references and introductory descriptions for techniques and findings I will need to incorporate into the planning stages (at least) of my future studies in the polar desert. In particular, the molecular approach to the phylogenetics and biodiversity of the soil photoautotrophs seems both powerful and relatively uncomplicated. There are many procedures to carry out, to be sure, but the justification for each is clear, and the sequence of operations appears to be linear.
These authors measured photosynthetic carbon fixation and microbial community composition in sub-nival barren soils in the Colorado Front Range of the United States, at 40ºN latitude and approximately 3600m altitude. Like polar desert soils, these sub-nival soils lack conspicuous macrophytic vegetation (vascular plants and bryophytes) and are snow-covered for most of the year. Previous examinations of these systems had suggested the majority of carbon input to these soils was derived from wind-blown dust, but this study demonstrated a much larger input of carbon from in-situ photosynthesis.
Net carbon fixation was estimated by subtracting in-light measurements from in-dark measurements of CO2 flux. All measurements were made using an IRGA system with a 1.18L transparent chamber; dark measurements were made by covering the chamber with a dark, opaque cloth. After measurement of CO2 flux, one site was carefully dug up and transported to the laboratory for molecular-phylogenetic analysis.
The soil was divided into 2 depths: 0-2cm and 2-4cm, then DNA was extracted and PCR using universal bacterial primers for the 16s region was carried out, followed by sequencing. This generated more than 1000 sequences, in 4 bacterial divisions containing known photoautotrophic microorganisms, plus some sequences from eukaryotic green algae.
The most intriguing group of bacteria found were the Chloroflexi, an understudied group found in both depth layers. The taxa composition found in the deeper layer was highly different from the community found in the surface, light-receiving zone, and the authors suggest, based on a few studies done of Chloroflexi in hot-springs environments, that this group may use longer-wavelength light which penetrates deeper in soils. These authors do not make it, but this suggests to me the microphotoautotrophs in this system may be partitioning their environment in both space (depth) and spectrum (red).
This paper includes a large number of references and introductory descriptions for techniques and findings I will need to incorporate into the planning stages (at least) of my future studies in the polar desert. In particular, the molecular approach to the phylogenetics and biodiversity of the soil photoautotrophs seems both powerful and relatively uncomplicated. There are many procedures to carry out, to be sure, but the justification for each is clear, and the sequence of operations appears to be linear.
Uchida et al. 2002
Uchida M, Muraoka H, Nakatsubo T, Bekku Y, Ueno T, Kanda H, Koizumi H. 2002. Net photosynthesis, respiration, and production of the moss Sanionia uncinata on a glacier foreland in the High Arctic, Ny-Ålesund, Svalbard. Arctic, Antarctic, and Alpine Research 34: 287-292.
These authors constructed a model of moss physiology that uses meteorological data to estimate productivity, based on data collected during one field season at Svalbard. In 2000, these authors measured the response of a common High Arctic moss species to water content, temperature, and light, then determined the relationship between those variables and available meteorological data, then applied previous-years meteorological data to their model and estimated previous-years productivity. These estimates suggest a great deal of variation in year-to-year productivity, driven largely by differences in water availability. Water content of fresh moss tissue was the single most important controlling variable in moss photosynthesis rates. The response to temperature was nearly flat between 7 and 23ºC, with near-freezing photosynthetic rates still a large fraction of maximum under saturating light conditions. Saturating light conditions were estimated at near 800µmol/m^2/s, which is not uncommon on sunny days in this environment.
The glacial foreground in question is at 79º North, but is not polar desert as it receives approximately 360mm of precipitation per year. The moss species studied is dominant in the local ecosystem, but appears to represent an intermediate successional stage, with high-productivity vascular plants replacing bryophytes in older sites in the area (i.e. further from the toe of the glacier).
These authors constructed a model of moss physiology that uses meteorological data to estimate productivity, based on data collected during one field season at Svalbard. In 2000, these authors measured the response of a common High Arctic moss species to water content, temperature, and light, then determined the relationship between those variables and available meteorological data, then applied previous-years meteorological data to their model and estimated previous-years productivity. These estimates suggest a great deal of variation in year-to-year productivity, driven largely by differences in water availability. Water content of fresh moss tissue was the single most important controlling variable in moss photosynthesis rates. The response to temperature was nearly flat between 7 and 23ºC, with near-freezing photosynthetic rates still a large fraction of maximum under saturating light conditions. Saturating light conditions were estimated at near 800µmol/m^2/s, which is not uncommon on sunny days in this environment.
The glacial foreground in question is at 79º North, but is not polar desert as it receives approximately 360mm of precipitation per year. The moss species studied is dominant in the local ecosystem, but appears to represent an intermediate successional stage, with high-productivity vascular plants replacing bryophytes in older sites in the area (i.e. further from the toe of the glacier).
Monday, September 21, 2009
Pilegaard et al. 2006
Pilegaard K, Skiba U, Ambus P, Beier C, Bruggemann N, Butterbach-Bahl, Dick J, Dorsey J, Duyzer J, Gallagher M, Gasche R, Horvath L, Kitzler B, Leip A, Pihlatie MK, Rosenkranz P, Seufert G, Vesala T, Westrate H, Zechmeister-Boltenstern S. 2006. Factors controlling regional differences in forest soil emission of nitrogen oxides (NO and N2O). Biogeosciences 3: 651-661.
These (abundant) authors present an analysis of a large combined dataset covering NO and N2O emissions from a range of forest systems in Europe. The measurements contributing to this large dataset were continuous measures (at least daily, usually hourly or better) and run at least one year. This provides a high-quality dataset that includes variation induced by seasonality.
One of the most interesting findings in this study is a scale-dependent relationship between soil parameters and N2O emissions. Within-forests, soil temperature and moisture were highly predictive of N2O flux, but not at scales encompassing multiple forests in comparison. At larger spatial scales, stand age and C/N ratio were much better predictors.
These (abundant) authors present an analysis of a large combined dataset covering NO and N2O emissions from a range of forest systems in Europe. The measurements contributing to this large dataset were continuous measures (at least daily, usually hourly or better) and run at least one year. This provides a high-quality dataset that includes variation induced by seasonality.
One of the most interesting findings in this study is a scale-dependent relationship between soil parameters and N2O emissions. Within-forests, soil temperature and moisture were highly predictive of N2O flux, but not at scales encompassing multiple forests in comparison. At larger spatial scales, stand age and C/N ratio were much better predictors.
Friday, September 4, 2009
Broll et al. 1999
Broll G, Tarnocai C, Mueller G. 1999. Interactions between vegetation, nutrients and moisture in soils in the Pangnirtung Pass area, Baffin island, Canada. Permafrost and Periglacial Processes 10: 265-277.
These authors examined soils from 6 pedons in Pangnirtung Pass, a north-south pass between mountains on Cumberland Peninsula. Three pedons were from moist soils, and three from dry soils. The moisture content drove a major difference in soil structure: dry soils are not cryoturbated, resulting in strong differences in nutrient content and mineralization rates.
The goal of the study was to compare in detail these differences between dry and moist soils. This seems very similar to my PhD goals surrounding examinations of Polar Desert soils. This study thus represents a possible template for some of my own investigations.
These authors examined soils from 6 pedons in Pangnirtung Pass, a north-south pass between mountains on Cumberland Peninsula. Three pedons were from moist soils, and three from dry soils. The moisture content drove a major difference in soil structure: dry soils are not cryoturbated, resulting in strong differences in nutrient content and mineralization rates.
The goal of the study was to compare in detail these differences between dry and moist soils. This seems very similar to my PhD goals surrounding examinations of Polar Desert soils. This study thus represents a possible template for some of my own investigations.
Tuesday, August 12, 2008
Michelutti et al. 2007
Michelutti N, Douglas MSV, Smol JP. 2007. Evaluating diatom community composition in the absence of marked limnological gradients in the high Arctic: a surface sediment calibration set from Cornwallis Island (Nunavut, Canada). Polar Biology 30: 1459-1473.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
Friday, August 8, 2008
Vermeij and Roopnarine 2008
Vermeij GJ, Roopnarine PD. 2008. The coming arctic invasion. Science 321: 780-781.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
Wednesday, June 4, 2008
Bell and Collins 2008
Bell G, Collins S. 2008. Adaptation, extinction and global change. Evolutionary Applications 1: 3-16.
These authors review and synthesize the current theory surrounding evolutionary responses to gradual environmental changes, especially increasing atmospheric carbon dioxide concentrations. In this context, these authors argue that the primary task of evolutionary biologists in the early 21st century is to predict adaptive evolution (or extinction) of populations and species in a gradually changing environment.
Populations are assumed to have high fitness, based on historical events. In a stable environment, beneficial alleles will accumulate, thus environmental changes are likely to be changes to the worse. Additionally, populations that do not adapt will suffer gradually declining mean fitness as pathogens and predators should themselves be selected for the most common target genotype.
Environmental variance increases with increasing time scales, that is, events occurring more distantly in time will be more different from each other. This applies to environmental conditions as much as anything else. The major implication of this in the context of this paper is that lineages surviving over long time periods will experience increasingly variable conditions, which also means generally deteriorating conditions if populations start well-adapted.
Many previous studies have found either strong selection, and / or high heritability. This apparent contradiction can be explained by high variability in the direction and magnitude of selection, suggesting that environmental variability is ubiquitous.
Populations can respond to changing conditions in four ways: phenotypic plasticity, dispersal and migration, adaptation, or extinction. These are arranged in order from short time scales to long.
The current pace of global environmental conditions change is probably higher than in most or all previous episodes. Historical levels of CO2 were about 280 ppm (parts per million); currently they are about 380 ppm, with some projections as high as 1000 ppm within the next 100 years.
These authors analysed the effects of the severity and frequency of environmental change (always change for the worse). They found that frequency is much more important to the probability of adaptation or “evolutionary rescue” than is severity. Frequent changes in conditions is likely to lead to extinction because selection does not have enough time to fix beneficial alleles, such that some fraction of the population is not well adapted to start with when the next change hits. In contrast, rare but severe changes lead to strong selection, and expose a long series of potentially beneficial alleles, increasing the mutation supply rate. The mutation supply rate is the critical parameter in determining adaptation or extinction, specifically the fraction of the supply of mutations that are beneficial and can rescue a declining population, i.e. raise a genotype’s rate of growth from negative to positive. Even rapid environmental change can be adapted to if the (rescue) mutation supply is high enough.
A survey of both simulations and studies of natural and laboratory populations revealed several cases of adaptation to frequent or continuous environmental change, and several cases of failure to adapt, even in species with very large population sizes. This indicates primarily that the rate of rescue mutations is unknown, despite being the single most important variable in predicting the evolutionary fates of populations under global climate change. However, these authors argue that a rescue mutation rate of approximately one per generation, regardless of population size, is probably close to the critical value, but qualify this estimate by stating they intend it as a first guess, and stimulus for more exact research in future.
The current driver of global environmental change is increasing CO2 concentrations in the atmosphere. Unlike most other agents of environmental change, CO2 is not in itself likely to represent a lethal stress to organisms, rather the effects will be either direct and positive (increased photosynthesis), or indirect via either temperature and climate changes or via biotic interactions such as competition.
Experiments and simulations by these and other authors have suggested that the short-term physiological responses of phytoplankton to increased CO2 will be opposite in direction to long-term evolutionary responses; this is at least partly because phytoplankton appear to be not limited by CO2 for growth. More specifically, the CO2-importing pump, which is tightly regulated by CO2 concentrations, will become less efficient, removing much of the productivity gain that would otherwise be predicted. Evidence that this will lead to community-level effects such as succession is currently equivocal, and based on short-term studies or idiosyncratic species compositions.
Our current understanding of evolution and ecology is based on populations subjected to a sudden shift from one stable environment to another, and usually a shift to increased stress or scarcity. In contrast, current global change is gradual and continuous, and is a case of nutrient enrichment.
These authors conclude with three main points. First, rescue mutations are critical to the phenomenon of evolutionary rescue and adaptation, but their rate is almost totally unknown. Second, the evolutionary response to increasing atmospheric CO2 concentrations is likely to be reduced efficiency of photosynthesis, rather than increased productivity. Third, these authors urge a general increase in studies of the evolutionary effects of global change, at rates of environmental change between the very fast rates typical of laboratory experimental evolution, and the very slow rates typical of most of the Earth’s history.
These authors review and synthesize the current theory surrounding evolutionary responses to gradual environmental changes, especially increasing atmospheric carbon dioxide concentrations. In this context, these authors argue that the primary task of evolutionary biologists in the early 21st century is to predict adaptive evolution (or extinction) of populations and species in a gradually changing environment.
Populations are assumed to have high fitness, based on historical events. In a stable environment, beneficial alleles will accumulate, thus environmental changes are likely to be changes to the worse. Additionally, populations that do not adapt will suffer gradually declining mean fitness as pathogens and predators should themselves be selected for the most common target genotype.
Environmental variance increases with increasing time scales, that is, events occurring more distantly in time will be more different from each other. This applies to environmental conditions as much as anything else. The major implication of this in the context of this paper is that lineages surviving over long time periods will experience increasingly variable conditions, which also means generally deteriorating conditions if populations start well-adapted.
Many previous studies have found either strong selection, and / or high heritability. This apparent contradiction can be explained by high variability in the direction and magnitude of selection, suggesting that environmental variability is ubiquitous.
Populations can respond to changing conditions in four ways: phenotypic plasticity, dispersal and migration, adaptation, or extinction. These are arranged in order from short time scales to long.
The current pace of global environmental conditions change is probably higher than in most or all previous episodes. Historical levels of CO2 were about 280 ppm (parts per million); currently they are about 380 ppm, with some projections as high as 1000 ppm within the next 100 years.
These authors analysed the effects of the severity and frequency of environmental change (always change for the worse). They found that frequency is much more important to the probability of adaptation or “evolutionary rescue” than is severity. Frequent changes in conditions is likely to lead to extinction because selection does not have enough time to fix beneficial alleles, such that some fraction of the population is not well adapted to start with when the next change hits. In contrast, rare but severe changes lead to strong selection, and expose a long series of potentially beneficial alleles, increasing the mutation supply rate. The mutation supply rate is the critical parameter in determining adaptation or extinction, specifically the fraction of the supply of mutations that are beneficial and can rescue a declining population, i.e. raise a genotype’s rate of growth from negative to positive. Even rapid environmental change can be adapted to if the (rescue) mutation supply is high enough.
A survey of both simulations and studies of natural and laboratory populations revealed several cases of adaptation to frequent or continuous environmental change, and several cases of failure to adapt, even in species with very large population sizes. This indicates primarily that the rate of rescue mutations is unknown, despite being the single most important variable in predicting the evolutionary fates of populations under global climate change. However, these authors argue that a rescue mutation rate of approximately one per generation, regardless of population size, is probably close to the critical value, but qualify this estimate by stating they intend it as a first guess, and stimulus for more exact research in future.
The current driver of global environmental change is increasing CO2 concentrations in the atmosphere. Unlike most other agents of environmental change, CO2 is not in itself likely to represent a lethal stress to organisms, rather the effects will be either direct and positive (increased photosynthesis), or indirect via either temperature and climate changes or via biotic interactions such as competition.
Experiments and simulations by these and other authors have suggested that the short-term physiological responses of phytoplankton to increased CO2 will be opposite in direction to long-term evolutionary responses; this is at least partly because phytoplankton appear to be not limited by CO2 for growth. More specifically, the CO2-importing pump, which is tightly regulated by CO2 concentrations, will become less efficient, removing much of the productivity gain that would otherwise be predicted. Evidence that this will lead to community-level effects such as succession is currently equivocal, and based on short-term studies or idiosyncratic species compositions.
Our current understanding of evolution and ecology is based on populations subjected to a sudden shift from one stable environment to another, and usually a shift to increased stress or scarcity. In contrast, current global change is gradual and continuous, and is a case of nutrient enrichment.
These authors conclude with three main points. First, rescue mutations are critical to the phenomenon of evolutionary rescue and adaptation, but their rate is almost totally unknown. Second, the evolutionary response to increasing atmospheric CO2 concentrations is likely to be reduced efficiency of photosynthesis, rather than increased productivity. Third, these authors urge a general increase in studies of the evolutionary effects of global change, at rates of environmental change between the very fast rates typical of laboratory experimental evolution, and the very slow rates typical of most of the Earth’s history.
Saturday, May 17, 2008
Briones et al. 2007
Briones MJI, Ineson P, Heinemeyer A. 2007. Predicting potential impacts of climate change on the geographical distribution of enchytraeids: a meta-analysis approach. Global Change Biology 13: 2252-2269.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
Wednesday, April 30, 2008
Olsson 1981
Olsson TI. 1981. Overwintering of benthic macroinvertebrates in ice and frozen sediment in a North Swedish river. Holarctic Ecology 4: 161-166.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
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