Huang Y, Zou J, Zheng X, Wang Y, Xu X. 2004. Nitrous oxide emissions as influenced by amendment of plant residues with different C:N ratios. Soil Biology & Biochemistry 36: 973-981.
These authors examined the role of residue quality, in the form of C:N ratio and a range of crop residues, on N2O emissions from soils. They also measured CO2 emissions, and found strong correlations between organic-matter decomposition and respiration, and nitrogen cycling.
Gas fluxes of CO2 and N2O were highly correlated across all incubations. To ensure only respiration-derived CO2 was measured, the CO2 released by urea breakdown in urea-treated treatments was calculated and subtracted; respiration in the urea-only treatment was similar to that in the untreated controls. Both gas emissions were negatively correlated with residue C:N ratios. Finally, residue C:N ratios were negatively correlated with dissolved organic carbon concentrations.
Overall, higher C:N ratios in residues seem to result in slow decomposition of mainly recalcitrant organic matter, and low CO2 and N2O emissions. Addition of urea in conjunction with crop residues produces a range of N2O emissions depending on the C:N ratio of the residues.
This short paper may serve as a model for the work I will be doing in the special topics class in soil science, fall 2010.
Showing posts with label Papers my coworkers may be interested in. Show all posts
Showing posts with label Papers my coworkers may be interested in. Show all posts
Tuesday, September 28, 2010
Trinsoutrot et al. 2000
Trinsoutrot I, Recous S, Mary B, Nicolardot B. 2000. C and N fluxes of decomposing 13C and 15N Brassica napus L.: effects of residue composition and N content. Soil Biology and Biochemistry 32: 1717-1730.
These authors studied the decomposition process by soil microorganisms when isotope-labelled crop residues were added to soil. The crop used, oilseed rape Brassica napus (also known as canola) varies its nitrogen content of tissues, and the C:N ratio, depending on levels of N inputs by fertilization. This allows variation in input organic matter quality by manipulation of growing conditions; in this experiment, both carbon and nitrogen inputs to the plant included stable-isotope labels, in the form of 13C-CO2 and 15N-KNO3. Plant residues were added to soils and incubated for 168 days.
Initial C:N ratio and especially the labile-C fraction of organic-matter inputs are major controls of both the rate of decomposition and fate of matter through the system. Additionally, temperature, particle size of residues, and water content in the soil also strongly influence decomposition processes.
Here, N mineralization (the formation of NO3- and NH4+ pools in the soil from organic-N precursors) occurred in two phases. In the early phase, up to about 3 weeks, the N cycle resulted in net mineralization. Later, mineral N pools were depleted and N was immobilized, that is, incorporated into the tissues of microbial cells.
Carbon dioxide release during the experiment occurred through two pathways. The more direct route was rapid mineralization of organic matter, which I interpret as non-incorporation of organic matter by microbes, consuming such material but metabolizing it rapidly through respiration. The second, presumably slower route was through metabolization of material after incorporation into cells through respiration. Either way, the ultimate fate of much of the organic-C in the residues was release as CO2.
Differences in the N-content of residues affected decomposition rates early in the experiment, but by about 4 months the differences between high-N and low-N residues had evened out. Only a small fraction of labelled N from residues ended up in soil mineral-N pools; the majority was either immobilized into microbial cells or remained in recalcitrant organic matter fractions. Immobilization of unlabeled, SOM-derived N was enhanced by the addition of C through a substitution effect.
These authors conclude that 15N labelling was fraught with difficulties, and both under- and overestimated some pools and processes. However, the use of their model, named NCSOIL, improved their ability to trace the fate of added material through the system. This paper represents a study similar in some ways to our planned course activity in the special topics in soil science course, fall 2010.
These authors studied the decomposition process by soil microorganisms when isotope-labelled crop residues were added to soil. The crop used, oilseed rape Brassica napus (also known as canola) varies its nitrogen content of tissues, and the C:N ratio, depending on levels of N inputs by fertilization. This allows variation in input organic matter quality by manipulation of growing conditions; in this experiment, both carbon and nitrogen inputs to the plant included stable-isotope labels, in the form of 13C-CO2 and 15N-KNO3. Plant residues were added to soils and incubated for 168 days.
Initial C:N ratio and especially the labile-C fraction of organic-matter inputs are major controls of both the rate of decomposition and fate of matter through the system. Additionally, temperature, particle size of residues, and water content in the soil also strongly influence decomposition processes.
Here, N mineralization (the formation of NO3- and NH4+ pools in the soil from organic-N precursors) occurred in two phases. In the early phase, up to about 3 weeks, the N cycle resulted in net mineralization. Later, mineral N pools were depleted and N was immobilized, that is, incorporated into the tissues of microbial cells.
Carbon dioxide release during the experiment occurred through two pathways. The more direct route was rapid mineralization of organic matter, which I interpret as non-incorporation of organic matter by microbes, consuming such material but metabolizing it rapidly through respiration. The second, presumably slower route was through metabolization of material after incorporation into cells through respiration. Either way, the ultimate fate of much of the organic-C in the residues was release as CO2.
Differences in the N-content of residues affected decomposition rates early in the experiment, but by about 4 months the differences between high-N and low-N residues had evened out. Only a small fraction of labelled N from residues ended up in soil mineral-N pools; the majority was either immobilized into microbial cells or remained in recalcitrant organic matter fractions. Immobilization of unlabeled, SOM-derived N was enhanced by the addition of C through a substitution effect.
These authors conclude that 15N labelling was fraught with difficulties, and both under- and overestimated some pools and processes. However, the use of their model, named NCSOIL, improved their ability to trace the fate of added material through the system. This paper represents a study similar in some ways to our planned course activity in the special topics in soil science course, fall 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.
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.
Wednesday, August 13, 2008
Reiss et al. 1995
Reiss RA, Schwert DP, Ashworth AC. 1995. Field preservation of Coleoptera for molecular genetic analyses. Environmental Entomology 24: 716-719.
These authors tested five preservatives for nuclear and mitochondrial DNA preservation. Carabid beetles collected at Kuujjuarapik, Quebec, from shore-line debris on Hudson Bay were placed into either 95% ethanol, Carnoy fixative (3:1 methanol:acetic acid), DNA isolation buffer (half whole, half homogenized with a pestle), cryotubes immersed in liquid nitrogen followed by storage at -80°C, or glass vials containing tissue paper soaked in ethyl acetate; all treatments except liquid nitrogen were at room temperature. Ethanol is widely used as both a fixative and a preservative, though it does often distort or remove body colouration, and is considered a hazardous material for transport. Ethyl acetate is sometimes used by entomologists to preserve morphology, as it causes less distortion than other techniques such as drying (pinned) or ethanol.
Overall, cryopreservation performed best, producing excellent results when the specimens were subjected to DNA extraction and basic molecular techniques examining both nuclear and mitochondrial DNA. Ethanol also performed well, though specimens maintained in ethanol longer than about 6 weeks showed significant degradation. DNA isolation buffer also performed well, as long as specimens were very thoroughly ground and homogenized; intact specimens did not yield good results.
These authors recommend ethanol for remote field studies where the equipment associated with liquid nitrogen would be very difficult to transport and maintain, and DNA isolation buffer combined with thorough grinding where ethanol cannot be carried due to its hazardous nature.
These authors tested five preservatives for nuclear and mitochondrial DNA preservation. Carabid beetles collected at Kuujjuarapik, Quebec, from shore-line debris on Hudson Bay were placed into either 95% ethanol, Carnoy fixative (3:1 methanol:acetic acid), DNA isolation buffer (half whole, half homogenized with a pestle), cryotubes immersed in liquid nitrogen followed by storage at -80°C, or glass vials containing tissue paper soaked in ethyl acetate; all treatments except liquid nitrogen were at room temperature. Ethanol is widely used as both a fixative and a preservative, though it does often distort or remove body colouration, and is considered a hazardous material for transport. Ethyl acetate is sometimes used by entomologists to preserve morphology, as it causes less distortion than other techniques such as drying (pinned) or ethanol.
Overall, cryopreservation performed best, producing excellent results when the specimens were subjected to DNA extraction and basic molecular techniques examining both nuclear and mitochondrial DNA. Ethanol also performed well, though specimens maintained in ethanol longer than about 6 weeks showed significant degradation. DNA isolation buffer also performed well, as long as specimens were very thoroughly ground and homogenized; intact specimens did not yield good results.
These authors recommend ethanol for remote field studies where the equipment associated with liquid nitrogen would be very difficult to transport and maintain, and DNA isolation buffer combined with thorough grinding where ethanol cannot be carried due to its hazardous nature.
Sunday, May 18, 2008
Krishan 1990
Krishan A. 1990. Rapid DNA content analysis by the Propidium iodide-hypotonic citrate method. Methods in Cell Biology 33: 121-125.
This author describes a set of protocols for staining nuclear DNA with Propidium iodide for use in flow cytometry. The basic protocol is similar to the methods we use in our lab currently, though this author claims that prepared stain solution can be stored at room temperature in a light-proof bottle in a large volume (e.g. 1 L), and that stained specimens can be stored up to 24 hours on ice without noticeable impact on measurements. Trypsin and heparin, frequently used in cell dissociation or blood storage procedures, will interfere with the binding of Propidium iodide to nuclear DNA.
This author describes a set of protocols for staining nuclear DNA with Propidium iodide for use in flow cytometry. The basic protocol is similar to the methods we use in our lab currently, though this author claims that prepared stain solution can be stored at room temperature in a light-proof bottle in a large volume (e.g. 1 L), and that stained specimens can be stored up to 24 hours on ice without noticeable impact on measurements. Trypsin and heparin, frequently used in cell dissociation or blood storage procedures, will interfere with the binding of Propidium iodide to nuclear DNA.
Tuesday, May 13, 2008
Leslie et al. 1997
Leslie AJ, Crisman TL, Prenger JP, Ewel KC. 1997. Benthic macroinvertebrates of small Florida pondcypress swamps and the influence of dry periods. Wetlands 17: 447-455.
These authors examined the faunas of three pondcypress swamps in northeastern Florida, over about 18 months from 1993 to 1995. Pondcypress swamps are wetlands with unpredictably-fluctuating water levels and a canopy formed by pondcypress trees (Taxodium distichum var. nutans). These swamps may remain wet for years or dry repeatedly within a single year, presenting a very challenging abiotic environment to aquatic organisms. Prior to this study, there had been few papers describing the biodiversity of pondcypress swamps, particularly during dry periods referred to as “drawdowns”.
The three ponds differed from each other in area, depth, and most dramatically emergent macrophyte vegetation. All three contained large abundances of Sphagnum mosses, and responded to local weather conditions similarly, tending to be driest at the same time, in June 1994. All ponds were highly acidic, with pH ranging between 3.4 and 4.4, and changing over time.
Benthic macroinvertebrates were collected by cores in a random fashion, to allow calculation of species richness and individual density per unit area, in this case reported as per square meter. Collected animals were identified to genus when possible using a range of identification keys from the literature (e.g. Pennak 1978). The beetle families Dytiscidae and Hydrophilidae and the fly family Chironomidae contributed large numbers of genera, and two genera of chironomids and one amphipod genus (Crangonyx) contributed the majority of individuals. Up to 52% of total individuals collected were specimens of Crangonyx.
Total species richness varied between the three pools, with the pool with least emergent vegetation having the lowest richness. Species richnesses were higher than those reported for other wetland habitats in the same region.
The authors report some surprise at the levels of biodiversity maintained even during dry periods. There is some speculation based on Barlocher et al. (1978) that drawdown periods are accompanied by an increase in bacterial and fungal activity, with a net increase in protein levels and therefore food quality in the detritus that forms the bulk of the food of most of the collected animals. Crangonyx and many of the other species found are generalists, and can cope with unpredictable dry periods by burrowing into wet soil or escaping to other habitats, while many of the species excluded during dry periods are obligate aquatics or have restricted life cycles and require a certain minimum period of wetness to complete one or more stages of the life cycle.
The high species richness of Dytiscidae and high population densities of Crangonyx are good indications for my project, as I expect to visit such habitats during the summer of 2008.
These authors examined the faunas of three pondcypress swamps in northeastern Florida, over about 18 months from 1993 to 1995. Pondcypress swamps are wetlands with unpredictably-fluctuating water levels and a canopy formed by pondcypress trees (Taxodium distichum var. nutans). These swamps may remain wet for years or dry repeatedly within a single year, presenting a very challenging abiotic environment to aquatic organisms. Prior to this study, there had been few papers describing the biodiversity of pondcypress swamps, particularly during dry periods referred to as “drawdowns”.
The three ponds differed from each other in area, depth, and most dramatically emergent macrophyte vegetation. All three contained large abundances of Sphagnum mosses, and responded to local weather conditions similarly, tending to be driest at the same time, in June 1994. All ponds were highly acidic, with pH ranging between 3.4 and 4.4, and changing over time.
Benthic macroinvertebrates were collected by cores in a random fashion, to allow calculation of species richness and individual density per unit area, in this case reported as per square meter. Collected animals were identified to genus when possible using a range of identification keys from the literature (e.g. Pennak 1978). The beetle families Dytiscidae and Hydrophilidae and the fly family Chironomidae contributed large numbers of genera, and two genera of chironomids and one amphipod genus (Crangonyx) contributed the majority of individuals. Up to 52% of total individuals collected were specimens of Crangonyx.
Total species richness varied between the three pools, with the pool with least emergent vegetation having the lowest richness. Species richnesses were higher than those reported for other wetland habitats in the same region.
The authors report some surprise at the levels of biodiversity maintained even during dry periods. There is some speculation based on Barlocher et al. (1978) that drawdown periods are accompanied by an increase in bacterial and fungal activity, with a net increase in protein levels and therefore food quality in the detritus that forms the bulk of the food of most of the collected animals. Crangonyx and many of the other species found are generalists, and can cope with unpredictable dry periods by burrowing into wet soil or escaping to other habitats, while many of the species excluded during dry periods are obligate aquatics or have restricted life cycles and require a certain minimum period of wetness to complete one or more stages of the life cycle.
The high species richness of Dytiscidae and high population densities of Crangonyx are good indications for my project, as I expect to visit such habitats during the summer of 2008.
Wednesday, April 9, 2008
Krasnov et al. 2008
Krasnov BR, Shenbrot GI, Khokhlova IS, Mouillot D, Poulin R. 2008. Latitudinal gradients in niche breadth: empirical evidence from haematophagous ectoparasites. Journal of Biogeography 35: 592-601.
This paper examined Rapoport’s rule in fleas that use small mammals in the Palaearctic as hosts, applying phylogenetic independent contrasts (PIC) to questions of geographic range size, latitude, and niche breadth. These authors consider Rapoport’s rule, of increased geographic range sizes with higher latitudes, to be a special case of a more general pattern of niche-breadth expansion (less specialization) with higher latitudes. Under this explanation, specialized species have narrow tolerances of abiotic conditions, use a small range of resources, and / or tolerant of a very limited set of competitors, predators, parasites, and diseases.
There is controversy in the current biogeographic literature about the extent of application of Rapoport’s rule or Rapoport’s effects. Some authors consider it a global phenomenon, driven by global mechanisms such orbital dynamics (Dynesius & Jansson, 2000) or habitat stability (MacArthur 1955; 1972) differences across the globe. Other authors, most notably Rhode (1996; 1999) consider Rapoport’s effects to be localized to only some latitudes or taxonomic groups.
Recently, Vazquez and Stevens (2004) presented a hypothesis for a mechanism underlying a global Rapoport’s rule. Briefly, they proposed that a positive relationship between niche breadth and latitude will occur if 1) there is a latitudinal gradient in species richness and 2) the species interaction network is an asymmetrically specialized interaction network such that specialists tend to interact with generalists. This hypotheses appears to involve the opposite direction of causality compared to hypotheses relating high tropical species richness to narrow species niches (i.e. high specialization) via character displacement and competitive exclusion.
The measure of niche breadth used in this study includes an estimate of the taxonomic distinctiveness of the fleas’ hosts. A flea species with a broad niche will use hosts that are more distantly related to each other than will a flea species with a narrow niche, even if both flea species use the same number of species of host. The authors describe this as the STD index, in which high values indicate more taxonomically distinct hosts such as hosts in different orders. In their analysis, these authors excluded all extreme specialist flea species, those found in only one geographic site or on only one mammal host species.
Analyses included regressions of two dependent variables (host specificity and geographic range size) against the independent variable (geographic range position) using both conventional statistics and PIC. Geographic range position was taken as the midpoint latitude of a species geographic range, which was computed by constructing minimum surface polygons and other techniques more fully described in their methods section.
Species level phylogenies were constructed for each family of fleas, based on a family-level phylogeny previously produced by Medvedev (1995) and morphological and taxonomic characters. Polytomies were considered “soft” i.e. they assumed no knowledge of hidden branching patterns. The PIC conducted by these authors included a range of sophisticated statistical controls, again more fully detailed in their methods section.
The results of this study demonstrate 1. fleas follow Rapoport’s rule, at least in the Palaearctic and 2. host specificity in fleas declines at higher latitudes. Thus the positive relationship in fleas of niche breadth and latitude holds for both abiotic (geographic range size) and biotic (diversity of hosts) components of their niches. There were some exceptions, but the overall trend is clear. These authors propose a mechanism underlying this trend that is much in line with Vazquez and Stevens (2004), involving interactions between niche breadth and geographic range and latitude and niche breadth.
This paper examined Rapoport’s rule in fleas that use small mammals in the Palaearctic as hosts, applying phylogenetic independent contrasts (PIC) to questions of geographic range size, latitude, and niche breadth. These authors consider Rapoport’s rule, of increased geographic range sizes with higher latitudes, to be a special case of a more general pattern of niche-breadth expansion (less specialization) with higher latitudes. Under this explanation, specialized species have narrow tolerances of abiotic conditions, use a small range of resources, and / or tolerant of a very limited set of competitors, predators, parasites, and diseases.
There is controversy in the current biogeographic literature about the extent of application of Rapoport’s rule or Rapoport’s effects. Some authors consider it a global phenomenon, driven by global mechanisms such orbital dynamics (Dynesius & Jansson, 2000) or habitat stability (MacArthur 1955; 1972) differences across the globe. Other authors, most notably Rhode (1996; 1999) consider Rapoport’s effects to be localized to only some latitudes or taxonomic groups.
Recently, Vazquez and Stevens (2004) presented a hypothesis for a mechanism underlying a global Rapoport’s rule. Briefly, they proposed that a positive relationship between niche breadth and latitude will occur if 1) there is a latitudinal gradient in species richness and 2) the species interaction network is an asymmetrically specialized interaction network such that specialists tend to interact with generalists. This hypotheses appears to involve the opposite direction of causality compared to hypotheses relating high tropical species richness to narrow species niches (i.e. high specialization) via character displacement and competitive exclusion.
The measure of niche breadth used in this study includes an estimate of the taxonomic distinctiveness of the fleas’ hosts. A flea species with a broad niche will use hosts that are more distantly related to each other than will a flea species with a narrow niche, even if both flea species use the same number of species of host. The authors describe this as the STD index, in which high values indicate more taxonomically distinct hosts such as hosts in different orders. In their analysis, these authors excluded all extreme specialist flea species, those found in only one geographic site or on only one mammal host species.
Analyses included regressions of two dependent variables (host specificity and geographic range size) against the independent variable (geographic range position) using both conventional statistics and PIC. Geographic range position was taken as the midpoint latitude of a species geographic range, which was computed by constructing minimum surface polygons and other techniques more fully described in their methods section.
Species level phylogenies were constructed for each family of fleas, based on a family-level phylogeny previously produced by Medvedev (1995) and morphological and taxonomic characters. Polytomies were considered “soft” i.e. they assumed no knowledge of hidden branching patterns. The PIC conducted by these authors included a range of sophisticated statistical controls, again more fully detailed in their methods section.
The results of this study demonstrate 1. fleas follow Rapoport’s rule, at least in the Palaearctic and 2. host specificity in fleas declines at higher latitudes. Thus the positive relationship in fleas of niche breadth and latitude holds for both abiotic (geographic range size) and biotic (diversity of hosts) components of their niches. There were some exceptions, but the overall trend is clear. These authors propose a mechanism underlying this trend that is much in line with Vazquez and Stevens (2004), involving interactions between niche breadth and geographic range and latitude and niche breadth.
Stork 2007
Stork NE. 2007. World of insects. Nature 448: 657-658.
This is a “News & Views” article in the August 9 2007 issue of Nature, summarizing and contrasting papers in that issue by Novotny et al. (2007) and Dyer et al. (2007).
Novotny et al. (2007) found low beta diversity, few barriers to dispersal, and low host specificity in tropical insects (primarily caterpillars) in Papua New Guinea. Dyer et al. (2007) found higher host specificity of caterpillars in tropical than in temperate South and North America. These apparently contradictory results are described by this author as requiring explanation derived from further large-scale, highly-cooperative studies in a similar vein as these described studies.
While I agree with this broad conclusion, I found this article somewhat annoying. An early section claims, without references, that up to 95% of insect species remain undescribed. However, Novotny et al. (2007) extensively discuss what they view as widely-publicized overestimates of global insect species richness, and suggest that total estimates should be revised downward from their currently-popular level of 10 million. A later section in Stork (2007) is little more than a rambling call for greater sampling effort of insects, other invertebrates, and other eukaryotes, particularly fungi, ending with a mention of the mid-domain “theory” (Colwell and Hartt, 1994); I was under the impression it was the mid-domain “hypothesis”, and was a useful null model for testing some large-scale biogeographic patterns.
This is a “News & Views” article in the August 9 2007 issue of Nature, summarizing and contrasting papers in that issue by Novotny et al. (2007) and Dyer et al. (2007).
Novotny et al. (2007) found low beta diversity, few barriers to dispersal, and low host specificity in tropical insects (primarily caterpillars) in Papua New Guinea. Dyer et al. (2007) found higher host specificity of caterpillars in tropical than in temperate South and North America. These apparently contradictory results are described by this author as requiring explanation derived from further large-scale, highly-cooperative studies in a similar vein as these described studies.
While I agree with this broad conclusion, I found this article somewhat annoying. An early section claims, without references, that up to 95% of insect species remain undescribed. However, Novotny et al. (2007) extensively discuss what they view as widely-publicized overestimates of global insect species richness, and suggest that total estimates should be revised downward from their currently-popular level of 10 million. A later section in Stork (2007) is little more than a rambling call for greater sampling effort of insects, other invertebrates, and other eukaryotes, particularly fungi, ending with a mention of the mid-domain “theory” (Colwell and Hartt, 1994); I was under the impression it was the mid-domain “hypothesis”, and was a useful null model for testing some large-scale biogeographic patterns.
Dyer et al. 2007
Dyer LA, Singer MS, Lill JT, Stireman JO, Gentry GL, Marquis RJ, Ricklefs RE, Greeney HF, Wagner DL, Morais HC, Diniz IR, Kursar TA, Coley PD. 2007. Host specificity of Lepidoptera in tropical and temperate forests. Nature 448: 696-700.
These authors examined thousands of species of caterpillars and host plants in the New World from southern Canada to Brazil. They were testing the hypothesis that greater niche specialization accounts for higher species richness in tropical regions. They measured ecological specialization along a latitudinal gradient by quantifying diet breadth in caterpillars and beta diversity of caterpillars on widespread focal tree species. Host plant specificity of forest caterpillars decreased with increasing latitude. They were able to control for varying sampling area and sampling effort, but not for phylogeny.
Possible explanations for this trend include the probability that tropical plants are chemically “nastier”, prompting stronger selection among herbivores for specialization in diet, under the assumption (not stated in this paper) that tradeoffs exist among strategies for dealing with plant chemical defences. The trend of increased tropical specialization could be strengthened if, as is likely, widespread and generalized tropical species are actually assemblies of cryptic specialists (i.e. conserved morphology but reproductive isolation and local specialization for diet). Additionally, temperate species of both Lepidoptera and trees are generally better-studied than their tropical counterparts, suggesting that many more species of highly specialized and possibly cryptic herbivores await description in the tropics.
This paper appears in an issue of Nature with a paper by Novotny et al. (2007). Both papers are summarized in a “News & Views” by Stork (2007), as they found apparently contradictory results.
These authors examined thousands of species of caterpillars and host plants in the New World from southern Canada to Brazil. They were testing the hypothesis that greater niche specialization accounts for higher species richness in tropical regions. They measured ecological specialization along a latitudinal gradient by quantifying diet breadth in caterpillars and beta diversity of caterpillars on widespread focal tree species. Host plant specificity of forest caterpillars decreased with increasing latitude. They were able to control for varying sampling area and sampling effort, but not for phylogeny.
Possible explanations for this trend include the probability that tropical plants are chemically “nastier”, prompting stronger selection among herbivores for specialization in diet, under the assumption (not stated in this paper) that tradeoffs exist among strategies for dealing with plant chemical defences. The trend of increased tropical specialization could be strengthened if, as is likely, widespread and generalized tropical species are actually assemblies of cryptic specialists (i.e. conserved morphology but reproductive isolation and local specialization for diet). Additionally, temperate species of both Lepidoptera and trees are generally better-studied than their tropical counterparts, suggesting that many more species of highly specialized and possibly cryptic herbivores await description in the tropics.
This paper appears in an issue of Nature with a paper by Novotny et al. (2007). Both papers are summarized in a “News & Views” by Stork (2007), as they found apparently contradictory results.
Novotny et al. 2007
Novotny V, Miller SE, Hulcr J, Drew RAI, Basset Y, Janda M, Setliff GP, Darrow K, Stewart AJA, Auga J, Isua B, Molem K, Manumbor M, Tamtiai E, Mogia M, Weiblen GD. 2007. Low beta diversity of herbivorous insects in tropical forests. Nature 448: 692-697.
These authors examined 370 species of caterpillars and about 130 species of ambrosia beetles (Scolytinae and Platypodinae) and fruitflies (Tephritidae) in a large contiguous patch of rainforest in Papua New Guinea. While total species richness was high, as expected for the tropics, beta diversity or turnover in species composition through space, was surprisingly low. The authors attribute this surprising finding primarily to the genus-specific rather than species-specific diets of many of the Lepidoptera. '
Beta diversity can be overestimated by inadequate sampling of many rare species, or underestimated by relying on taxonomically known species that tend to be the most widespread and abundant species. In this study, these issues were addressed by studying relatively well-described insect taxa on a limited subset of the available plant hosts, in this case four genera of trees including 175 species in the study area. Study sites were evenly distributed across a large area that was nearly homogeneous for altitude, climate, soil, vegetation, and other factors. In general, herbivore diversity tracked the diversity (alpha and beta) of their plant hosts, which in itself is a less than surprising finding. Other studies that have found high beta diversity of tropical insects have followed topological or climatic gradients, where plant host beta diversity is also high.'
This paper appears in the same issue of Nature as Dyer et al. (2007), and a “News & Views” commentary by Stork (2007). Dyer et al. (2007) found high beta diversity of tropical insects, but their study is different in many ways from that of Novotny et al. (2007).
These authors examined 370 species of caterpillars and about 130 species of ambrosia beetles (Scolytinae and Platypodinae) and fruitflies (Tephritidae) in a large contiguous patch of rainforest in Papua New Guinea. While total species richness was high, as expected for the tropics, beta diversity or turnover in species composition through space, was surprisingly low. The authors attribute this surprising finding primarily to the genus-specific rather than species-specific diets of many of the Lepidoptera. '
Beta diversity can be overestimated by inadequate sampling of many rare species, or underestimated by relying on taxonomically known species that tend to be the most widespread and abundant species. In this study, these issues were addressed by studying relatively well-described insect taxa on a limited subset of the available plant hosts, in this case four genera of trees including 175 species in the study area. Study sites were evenly distributed across a large area that was nearly homogeneous for altitude, climate, soil, vegetation, and other factors. In general, herbivore diversity tracked the diversity (alpha and beta) of their plant hosts, which in itself is a less than surprising finding. Other studies that have found high beta diversity of tropical insects have followed topological or climatic gradients, where plant host beta diversity is also high.'
This paper appears in the same issue of Nature as Dyer et al. (2007), and a “News & Views” commentary by Stork (2007). Dyer et al. (2007) found high beta diversity of tropical insects, but their study is different in many ways from that of Novotny et al. (2007).
Friday, April 4, 2008
Bennett et al. 2005
Bennett VA, Sformo T, Walters K, Toien O, Jeannet K, Hochstrasser R, Pan Q, Serianni AS, Barnes BM, Duman JG. 2005. Comparative overwintering physiology of Alaska and Indiana populations of the beetle Cucujus clavipes (Fabricius): roles of antifreeze proteins, polyols, dehydration and daipause. Journal of Experimental Biology 208: 4467-4477.
These authors measured various aspects of winter survival in the larvae of a bark-dwelling beetle, in two locations (Alaska and Indiana) over three years. These larvae produce antifreeze proteins (AFP) and polyols such as glycerol that lower their supercooling points considerably. Dehydration in Alaskan insects increases the haemolymph concentration of these AFPs and further depresses the supercooling point of body tissues. Previous reports of this species’ overwintering abilities suggested they were freeze tolerant, but this paper strongly suggests they are freeze avoiding, and may be capable of body water vitrification under some extreme circumstances.
To examine the distinction between freeze tolerance and freeze avoidance, these authors measured supercooling points, thermal hysteresis activity, body water content, polyols content, and respiration rates in larvae. Supercooling points were taken as the temperature at which exotherms were recorded, when the heat of fusion of water was released by ice formation. All larvae that produced exotherms died, while all larvae that were cooled to just above expected supercooling points but were not frozen survived. No larvae produced exotherms colder than -58°C, and about half of those cooled lower than this survived, which was taken by these authors as indirect evidence of body water vitrification. Further analyses would be necessary to confirm this suggestion.
The differences in survivability of winter temperatures shown by Alaskan and Indianan larvae may relate primarily to the timing of AFP production. Alaskan larvae synthesize AFPs much earlier in the season than do Indianan, and are capable of survival in Indiana while Indianan larvae all died when overwintered in Alaska. The extreme dehydration of Alaskan larvae prevented measurement of body water content and AFP concentration, thus the relative importance of amounts produced, timing of production, and duration and severity of winter could not be determined.
In summary, there appears to be a genetic component to differences in larval overwintering capabilities across this species’ very broad latitudinal range. The physiological mechanism of this difference, either timing, magnitude, or composition of the production of antifreeze molecules, is not clear.
These authors measured various aspects of winter survival in the larvae of a bark-dwelling beetle, in two locations (Alaska and Indiana) over three years. These larvae produce antifreeze proteins (AFP) and polyols such as glycerol that lower their supercooling points considerably. Dehydration in Alaskan insects increases the haemolymph concentration of these AFPs and further depresses the supercooling point of body tissues. Previous reports of this species’ overwintering abilities suggested they were freeze tolerant, but this paper strongly suggests they are freeze avoiding, and may be capable of body water vitrification under some extreme circumstances.
To examine the distinction between freeze tolerance and freeze avoidance, these authors measured supercooling points, thermal hysteresis activity, body water content, polyols content, and respiration rates in larvae. Supercooling points were taken as the temperature at which exotherms were recorded, when the heat of fusion of water was released by ice formation. All larvae that produced exotherms died, while all larvae that were cooled to just above expected supercooling points but were not frozen survived. No larvae produced exotherms colder than -58°C, and about half of those cooled lower than this survived, which was taken by these authors as indirect evidence of body water vitrification. Further analyses would be necessary to confirm this suggestion.
The differences in survivability of winter temperatures shown by Alaskan and Indianan larvae may relate primarily to the timing of AFP production. Alaskan larvae synthesize AFPs much earlier in the season than do Indianan, and are capable of survival in Indiana while Indianan larvae all died when overwintered in Alaska. The extreme dehydration of Alaskan larvae prevented measurement of body water content and AFP concentration, thus the relative importance of amounts produced, timing of production, and duration and severity of winter could not be determined.
In summary, there appears to be a genetic component to differences in larval overwintering capabilities across this species’ very broad latitudinal range. The physiological mechanism of this difference, either timing, magnitude, or composition of the production of antifreeze molecules, is not clear.
Wednesday, April 2, 2008
Piepenburg 2005
Piepenburg D. 2005. Recent research on Arctic benthos: common notions need to be revised. Polar Biology 28: 733-755.
This author reviews the broad scale ecology of Arctic marine benthic environments, with emphasis on energy and matter flows and biodiversity patterns. There is an early summary of what was known or supposed about Arctic benthic biodiversity in the late 1980s and early 1990s, before major shifts in research took place. With the breakup of the Soviet Union and concommitent opening to Western researchers of the Siberian Arctic, and an increased public awareness of polar issues, the mid-to-late 1990s saw a large increase in scientific attention on the Arctic benthos.
No single clear definition of “Arctic” for the marine realm is recognized, but this author follows the work of Zenkevitch (1963; original in Russian 1955), which broadly defines the Arctic marine as the Arctic Ocean proper, plus its adjacent seas including the northern shorelines of Eurasia and North America, as well as the continental shelves of Greenland, Baffin Bay, and everything north of the “Polar Front” of the Barents and Bering seas. A map of these areas is provided in figure 1.
While the Arctic Ocean proper is almost entirely covered by permanent sea-ice, the adjacent Arctic seas are primarily characterized by very low but relatively constant water temperatures, long-lasting seasonal ice cover, and very pronounced seasonal fluctuations in insolation and, hence, primary production. There are broad continental shelves underlying several Arctic seas such as the Laptev Sea of central Siberia, and these shelves receive a large amount of input from rivers, approximately 10% of the total global river outflow. The broad width of several of these shelves prevents movement of this terrestrial input into the deeper basins of the central Arctic ocean.
The Arctic as a low-temperature ecosystem is much younger than that of Antarctica. While a cold circumpolar current formed around Antarctica perhaps 23mya, the Arctic ocean was temperate until a drastic fall in sea temperatures in the Pliocene about 4mya. During that recent 4my, many areas of Arctic shelf have been either dry due to sea level falls, or covered by glaciers, effectively removing the benthic faunas. Many Antarctic shelf areas also probably experienced glaciation, sometimes to surprisingly deep depths of hundreds of meters. This pattern of repeated extermination and recolonization may imply that Arctic organisms are particularly resilient in the face of environmental change.
Work since the increase in Arctic research has generally supported but modified pre-existing views of Arctic ecology. Both the Arctic and Antarctic benthos can be considered to harbor intermediate biodiversity, though the Antarctic still appears to be slightly more diverse. Disturbances once thought to be unique to the Arctic (such as iceberg bottom-scouring) have been found at significant frequencies in the Antarctic. Most Arctic organisms appear to be wide-spread boreal-Arctic species rather than endemic, while much more of the Antarctic biota is endemic to areas south of the Antarctic convergence.
The major faunal groups of the Arctic benthos are:
On fine sand and mud, bivalves and polychaetes.
On coarse grained sediments, gammaridean amphipods.
On many shelf and slope habitats, brittle stars, which can reach carpet-like population densities.
In the Barents Sea, sea urchins
In the Laptev Sea, sea cucumbers and bivalves
In the Bearing and Chukchi Seas, sea stars and crustaceans, including dense populations of ampeliscid amphipods in some areas
In the deep ocean basins of the Arctic Ocean proper, deposit feeding polychaetes, crustaceans, and bivalves.
“Pelago-benthic coupling” is a blanket term coined by Hargrave (1973) to refer to the downward flux of matter and energy from the water column to the seabed, and related processes of upwelling and other mixing effects. This coupling seems especially strong and important in the Arctic ocean, with meso-scale variations (10-100km) driven by local bottom topology, currents, ice cover dynamics (including polynyas), et cetera. The stronger coupling in the Arctic appears to be driven by a slower response of zooplankton to seasonal changes in phytoplankton, allowing more “fresh” captured carbon to reach the sea floor.
The deep Arctic Ocean basins are apparently relatively uncoupled from adjacent shelf areas, with most productivity in the basins driven by very strong pelago-benthic coupling. Nonetheless, the Arctic Ocean supports productivity about an order of magnitude higher than previously suspected, in part due to the role of ice-bound algae and stochastic large inputs of food.
This is a useful review paper that introduces many of the issues of Arctic marine biology at an ecosystem scale. There are useful links here to other community ecology considerations and to deep ocean research programs.
This author reviews the broad scale ecology of Arctic marine benthic environments, with emphasis on energy and matter flows and biodiversity patterns. There is an early summary of what was known or supposed about Arctic benthic biodiversity in the late 1980s and early 1990s, before major shifts in research took place. With the breakup of the Soviet Union and concommitent opening to Western researchers of the Siberian Arctic, and an increased public awareness of polar issues, the mid-to-late 1990s saw a large increase in scientific attention on the Arctic benthos.
No single clear definition of “Arctic” for the marine realm is recognized, but this author follows the work of Zenkevitch (1963; original in Russian 1955), which broadly defines the Arctic marine as the Arctic Ocean proper, plus its adjacent seas including the northern shorelines of Eurasia and North America, as well as the continental shelves of Greenland, Baffin Bay, and everything north of the “Polar Front” of the Barents and Bering seas. A map of these areas is provided in figure 1.
While the Arctic Ocean proper is almost entirely covered by permanent sea-ice, the adjacent Arctic seas are primarily characterized by very low but relatively constant water temperatures, long-lasting seasonal ice cover, and very pronounced seasonal fluctuations in insolation and, hence, primary production. There are broad continental shelves underlying several Arctic seas such as the Laptev Sea of central Siberia, and these shelves receive a large amount of input from rivers, approximately 10% of the total global river outflow. The broad width of several of these shelves prevents movement of this terrestrial input into the deeper basins of the central Arctic ocean.
The Arctic as a low-temperature ecosystem is much younger than that of Antarctica. While a cold circumpolar current formed around Antarctica perhaps 23mya, the Arctic ocean was temperate until a drastic fall in sea temperatures in the Pliocene about 4mya. During that recent 4my, many areas of Arctic shelf have been either dry due to sea level falls, or covered by glaciers, effectively removing the benthic faunas. Many Antarctic shelf areas also probably experienced glaciation, sometimes to surprisingly deep depths of hundreds of meters. This pattern of repeated extermination and recolonization may imply that Arctic organisms are particularly resilient in the face of environmental change.
Work since the increase in Arctic research has generally supported but modified pre-existing views of Arctic ecology. Both the Arctic and Antarctic benthos can be considered to harbor intermediate biodiversity, though the Antarctic still appears to be slightly more diverse. Disturbances once thought to be unique to the Arctic (such as iceberg bottom-scouring) have been found at significant frequencies in the Antarctic. Most Arctic organisms appear to be wide-spread boreal-Arctic species rather than endemic, while much more of the Antarctic biota is endemic to areas south of the Antarctic convergence.
The major faunal groups of the Arctic benthos are:
On fine sand and mud, bivalves and polychaetes.
On coarse grained sediments, gammaridean amphipods.
On many shelf and slope habitats, brittle stars, which can reach carpet-like population densities.
In the Barents Sea, sea urchins
In the Laptev Sea, sea cucumbers and bivalves
In the Bearing and Chukchi Seas, sea stars and crustaceans, including dense populations of ampeliscid amphipods in some areas
In the deep ocean basins of the Arctic Ocean proper, deposit feeding polychaetes, crustaceans, and bivalves.
“Pelago-benthic coupling” is a blanket term coined by Hargrave (1973) to refer to the downward flux of matter and energy from the water column to the seabed, and related processes of upwelling and other mixing effects. This coupling seems especially strong and important in the Arctic ocean, with meso-scale variations (10-100km) driven by local bottom topology, currents, ice cover dynamics (including polynyas), et cetera. The stronger coupling in the Arctic appears to be driven by a slower response of zooplankton to seasonal changes in phytoplankton, allowing more “fresh” captured carbon to reach the sea floor.
The deep Arctic Ocean basins are apparently relatively uncoupled from adjacent shelf areas, with most productivity in the basins driven by very strong pelago-benthic coupling. Nonetheless, the Arctic Ocean supports productivity about an order of magnitude higher than previously suspected, in part due to the role of ice-bound algae and stochastic large inputs of food.
This is a useful review paper that introduces many of the issues of Arctic marine biology at an ecosystem scale. There are useful links here to other community ecology considerations and to deep ocean research programs.
Monday, March 31, 2008
Andrews and Rigler 1985
Andrews D, Rigler FH. 1985. The effects of an Arctic winter on benthic invertebrates in the littoral zone of Char Lake, Northwest Territories. Canadian Journal of Zoology 63: 2825-2834.
These authors examined the benthic invertebrates of Char Lake, near Resolute, Nunavut, during both summer and winter. Char Lake freezes to the bottom around its edge, to approximately 2.5m thickness. Surface ice melts first from the edges of the lake, and when the littoral zone is ice-free water temperatures may reach up to 6°C. Deeper areas do not freeze solid in winter, but may never experience total loss of ice cover in summer.
Animals can be roughly categorized as either freezing tolerant, in which ice crystals form inside the body, or as freezing susceptible, in which ice formation is prevented through supercooling. The surrounding liquid water of aquatic habitats may cause tissue freezing by providing nucleating ice crystals at low temperatures, thus aquatic organisms may not be able to supercool, and must therefore either be freezing tolerant or migrate to nonfrozen areas.
The purpose of this study was fourfold. 1. to determine the temperature conditions of the winter benthos in Char Lake; 2. to determine if animals trapped in the zone of freezing can survive; 3. to determine if emigration to deeper, nonfrozen waters occurs; 4. to determine the effects of subzero temperatures on a focus species of harpacticoid copepod.
This paper provides an excellent description of the physical environment of Char Lake, which is located near the Polar Continental Shelf Project in Resolute, and has been intensively studied by many researchers since approximately 1960.
These authors used two distinct sampling methods in summer and winter. Summer sampling of the benthos was by a vacuum system operated by SCUBA divers. Winter sampling was by retrieval of frozen baskets previously embedded in the substrate during summer dives. Plastic chips may still be present in Char Lake from the marker floats used on these benthic baskets, as retrieval was by drilling into the thick ice until the underwater float was reached, followed by expansion of the hole and chiselling out the frozen basket.
Specimens were thawed and examined for survival, though logistical considerations meant that some samples were not as rigorously controlled. Temperature profiles of the lake indicated that the thick layer of ice and snow provided significant insulation, with frozen benthic temperatures never lower than -7.5°C, even with atmospheric temperatures below -20°C. Waters deeper than about 2.5m did not freeze.
The focus harpacticoid species, Attheyella nordenskioldii, persists in Char Lake as two possibly distinct populations. In deeper waters, this species reproduces throughout the year, though most individuals overwinter as adults. In shallower waters, adults may freeze solid for up to 8 months every year, with much more synchronous development than the deeper-water individuals. Both putative populations show 1-year life cycles. The authors explore some hypotheses that could explain how the winter-inactive individuals are able to maintain the same life cycle timing as the winter-active individuals. These hypotheses primarily rest upon energetic considerations, such that the shallow water populations have a summer advantage of temperature and thus metabolic and development rates that can make up for the winter disadvantage of those rates.
Animals trapped in the frozen zone were able to survive, and special overwintering stages were found only in one species of chironomid; all other examined species did not show obvious morphological characteristics associated with overwinter, though it is possible that physiological modifications such as dehydration were occurring. These authors could not separate induced from natural mortality, but were confident that all examined species were capable of high survivorship each winter. Additionally, no significant emigration to deeper, nonfrozen areas was detected, though some levels of such migration probably do occur.
The final part of the discussion of this paper focuses on the different strategies of A. nordenskioldii, and suggests further research on the energetic ecology of this species, this lake, and other seasonally frozen environments is warranted.
Monday, March 17, 2008
Libertini et al. 2008
Libertini A, Trisolini R, Rampin M. 2008. Chromosome number, karyotype morphology, heterochromatin distribution and nuclear DNA content of some talitroidean amphipods (Crustacea: Gammaridea). European Journal of Entomology 105: 53-58.
These authors report genome size and other genomic phenotypes for 10 species of amphipods in the infraorder Talitrida, which includes family Hyalellidae and family Talitridae. Talitridae includes intertidal, supralitoral, and fully terrestrial species. The cytogenetics of this group of amphipods are poorly understood, with few species receiving significant scientifica attention to date.
Genome size and AT-content were measured by flow cytometry. Cell suspensions were prepared as in Libertini et al. (2000), primarily of either late embryos or pooled internal organs of adults. Genome sizes were larger in more terrestial species. Additionally, two species with the largest genomes in their respective families, that inhabit the high intertidal in the Mediterranean, shifted their habitats inland to fully terrestial in northern locations such as Iceland.
These patterns support the hypothesis applied to other amphibious or terrestrial-colonizing groups such as gastropods and sarcopterygian fishes, that large genome size is a pre-adaptation or associated with other pre-adaptations to terrestrial life. Additionally, the authors associate the harsh terrestrial environment, large genomes, and the harsher environments of higher latitudes, citing in particular Rees et al. (2007) and the discovery of very large amphipod genomes in Arctic environments.
These authors report genome size and other genomic phenotypes for 10 species of amphipods in the infraorder Talitrida, which includes family Hyalellidae and family Talitridae. Talitridae includes intertidal, supralitoral, and fully terrestrial species. The cytogenetics of this group of amphipods are poorly understood, with few species receiving significant scientifica attention to date.
Genome size and AT-content were measured by flow cytometry. Cell suspensions were prepared as in Libertini et al. (2000), primarily of either late embryos or pooled internal organs of adults. Genome sizes were larger in more terrestial species. Additionally, two species with the largest genomes in their respective families, that inhabit the high intertidal in the Mediterranean, shifted their habitats inland to fully terrestial in northern locations such as Iceland.
These patterns support the hypothesis applied to other amphibious or terrestrial-colonizing groups such as gastropods and sarcopterygian fishes, that large genome size is a pre-adaptation or associated with other pre-adaptations to terrestrial life. Additionally, the authors associate the harsh terrestrial environment, large genomes, and the harsher environments of higher latitudes, citing in particular Rees et al. (2007) and the discovery of very large amphipod genomes in Arctic environments.
Wilhelm et al. 2003
Wilhelm J, Pingoud A, Hahn M. 2003. Real-time PCR-based method for the estimation of genome sizes. Nucleic Acids Research 31: e56.
These authors describe and demonstrate a new method for genome size estimation, based on real-time PCR (RT-PCR). The RT-PCR process is used to count copies of a target sequence in a sample of genomic DNA of unknown genome size, simultaneously with the amplification of the same sequence in a standard DNA present in the same reaction tube. As with other methods of genome size estimation, the known standard is used to calculate the unknown genome size, though the actual calculation is different from that employed in flow cytometry or Feulgen image analysis densitometry.
Estimation by RT-PCR involves calculation of the unknown genome size by dividing the total mass of genomic DNA by the number of copies of the target sequence as detected by fluorescence during the amplification reactions. Typically, a target sequence that is known to exist one-copy-per-genome is used. The co-prepared standard is used to calibrate fluorescence intensity and copy number.
This method only works if two conditions can be met: a) the absolute copy number of the target sequence in the standard is known and b) the absolute mass concentration of the genomic DNA in the sample can be determined accurately. Both conditions can be met using the absorbance of the sample at 260 nm (UV-260 abs). Protein contamination will prevent accurate readings, and can be detected by determining the absorbance properties of the sample at the full range of wavelengths between 260 and 320 nm. RNA will also interfere with measurements, at it absorbs similarly to DNA at UV wavelengths; it should be removed with an exhaustive treatment of RNAase.
The copy-concentration of the standard can be determined from pure samples by dividing the measured mass of standard DNA by the known fragment size. To ensure accurate calibration, the standard’s sequence should be identical to the target sequence amplified from the unknown; thus the ideal standard is a fragment that contains the RT-PCR “inner primer” sites and is of known fragment length. This can be determined by gel electrophoresis if the primer positions are not already reliably known.
These authors conclude that RT-PCR genome size estimation is accurate, precise, and useful in situations where other techniques are impractical. For example, they state that it can be used on samples that cannot be used in flow cytometry. Though they provide no examples of such situations, I can think of at least one widespread condition: that of specimens preserved in ethanol with destroyed or damaged nuclei but undamaged DNA. These authors make no mention of their method’s relative advantages compared to Feulgen-based methods.
These authors describe and demonstrate a new method for genome size estimation, based on real-time PCR (RT-PCR). The RT-PCR process is used to count copies of a target sequence in a sample of genomic DNA of unknown genome size, simultaneously with the amplification of the same sequence in a standard DNA present in the same reaction tube. As with other methods of genome size estimation, the known standard is used to calculate the unknown genome size, though the actual calculation is different from that employed in flow cytometry or Feulgen image analysis densitometry.
Estimation by RT-PCR involves calculation of the unknown genome size by dividing the total mass of genomic DNA by the number of copies of the target sequence as detected by fluorescence during the amplification reactions. Typically, a target sequence that is known to exist one-copy-per-genome is used. The co-prepared standard is used to calibrate fluorescence intensity and copy number.
This method only works if two conditions can be met: a) the absolute copy number of the target sequence in the standard is known and b) the absolute mass concentration of the genomic DNA in the sample can be determined accurately. Both conditions can be met using the absorbance of the sample at 260 nm (UV-260 abs). Protein contamination will prevent accurate readings, and can be detected by determining the absorbance properties of the sample at the full range of wavelengths between 260 and 320 nm. RNA will also interfere with measurements, at it absorbs similarly to DNA at UV wavelengths; it should be removed with an exhaustive treatment of RNAase.
The copy-concentration of the standard can be determined from pure samples by dividing the measured mass of standard DNA by the known fragment size. To ensure accurate calibration, the standard’s sequence should be identical to the target sequence amplified from the unknown; thus the ideal standard is a fragment that contains the RT-PCR “inner primer” sites and is of known fragment length. This can be determined by gel electrophoresis if the primer positions are not already reliably known.
These authors conclude that RT-PCR genome size estimation is accurate, precise, and useful in situations where other techniques are impractical. For example, they state that it can be used on samples that cannot be used in flow cytometry. Though they provide no examples of such situations, I can think of at least one widespread condition: that of specimens preserved in ethanol with destroyed or damaged nuclei but undamaged DNA. These authors make no mention of their method’s relative advantages compared to Feulgen-based methods.
Friday, March 14, 2008
Conlan and Kvitek 2005
Conlan KE, Kvitek RG. 2005. Recolonization of soft-sediment ice scours on an exposed Arctic coast. Marine Ecology Progress Series 286: 21-42.
These authors monitored the occurrence, aging, and biotic recolonization of ice scours in the Barrow Strait near Resolute, Nunavut. Ice structures with deep keels, such as icebergs locked in pack ice, can scour the soft bottom even at depths approaching 100m. Scours can be 10 to 15 meters deep, hundreds of meters wide, and kilometers long, though many are smaller than that. A scour forms a characteristic geomorphology, with a deep trough that may include multiple parallel sub-troughs, bordered by berms that may be 4-5m tall relative to unscoured adjacent seabed. The benthos of Barrow Strait is hard-packed clay armored with cobble, a glacial till that lies about 5m thick above the bedrock.
Ice scours remove the cobble, and the berms are much softer than either the troughs or adjacent unscoured seabed. These authors, and a large crew of assistants, sampled the macroinvertebrates of the seabed by cores collected by SCUBA. The faunal analysis was by seiving the samples, fixing specimens in 4% Formalin and preserving them in 70% Ethanol. Most specimens were identified to family or genus, but a large sample of collected polychaetes were sent to experts in Ottawa for species-level identification. Faunal composition was compared across scours, troughs and berms, unscoured seabed, and scours of various ages, monitored over a 9-year period.
Biotically, the examined portion of the Barrow Strait constitues “urchin barrens”. Sea urchins, primarily Strongelocentrotus droebachiensis and S. pallidus, are present in high density and graze on most other epibenthic and shallow-infaunal invertebrates as well as consuming most of the available algae. The invasion by urchins may be recent, as suggested by the presence of Balanus crenatus only in areas where urchins are absent, but crushed shells of this barnacle in many areas. Other macroinvertebrates found included brittle stars, gastropods, soft corals, anenomes, sea cucumbers, etc, as well as several species of bottom dwelling fishes.
In general, the authors found a pattern of biodiversity consistent with the intermediate-disturbance hypothesis. Total species richness and biomass were both higher in areas of scours compared to unscoured areas. A patch of seabed protected from most scours behind a large berm had lower total diversity. No suite of climax species was found in any undisturbed area. One species of polychaete was found only in relatively young scours, but all other species occurred in all habitats, though relative abundances varied. This pattern suggests that ice scours and their associated habitat variation may be maintaining relatively high biodiversity in this region.
Ice scours occur with a frequency of about 1.1 events per kilometer per year, similar to some other ice-scoured habitats in other polar regions. This rate may either increase or decrease with climate warming. Warmer temperatures may increase the rate of iceberg calving, increasing the supply of deep-keel ice structures. Alternately, warmer temperatures may reduce the thickness, strength, or movements of winter pack ice and associated scouring structures.
These authors monitored the occurrence, aging, and biotic recolonization of ice scours in the Barrow Strait near Resolute, Nunavut. Ice structures with deep keels, such as icebergs locked in pack ice, can scour the soft bottom even at depths approaching 100m. Scours can be 10 to 15 meters deep, hundreds of meters wide, and kilometers long, though many are smaller than that. A scour forms a characteristic geomorphology, with a deep trough that may include multiple parallel sub-troughs, bordered by berms that may be 4-5m tall relative to unscoured adjacent seabed. The benthos of Barrow Strait is hard-packed clay armored with cobble, a glacial till that lies about 5m thick above the bedrock.
Ice scours remove the cobble, and the berms are much softer than either the troughs or adjacent unscoured seabed. These authors, and a large crew of assistants, sampled the macroinvertebrates of the seabed by cores collected by SCUBA. The faunal analysis was by seiving the samples, fixing specimens in 4% Formalin and preserving them in 70% Ethanol. Most specimens were identified to family or genus, but a large sample of collected polychaetes were sent to experts in Ottawa for species-level identification. Faunal composition was compared across scours, troughs and berms, unscoured seabed, and scours of various ages, monitored over a 9-year period.
Biotically, the examined portion of the Barrow Strait constitues “urchin barrens”. Sea urchins, primarily Strongelocentrotus droebachiensis and S. pallidus, are present in high density and graze on most other epibenthic and shallow-infaunal invertebrates as well as consuming most of the available algae. The invasion by urchins may be recent, as suggested by the presence of Balanus crenatus only in areas where urchins are absent, but crushed shells of this barnacle in many areas. Other macroinvertebrates found included brittle stars, gastropods, soft corals, anenomes, sea cucumbers, etc, as well as several species of bottom dwelling fishes.
In general, the authors found a pattern of biodiversity consistent with the intermediate-disturbance hypothesis. Total species richness and biomass were both higher in areas of scours compared to unscoured areas. A patch of seabed protected from most scours behind a large berm had lower total diversity. No suite of climax species was found in any undisturbed area. One species of polychaete was found only in relatively young scours, but all other species occurred in all habitats, though relative abundances varied. This pattern suggests that ice scours and their associated habitat variation may be maintaining relatively high biodiversity in this region.
Ice scours occur with a frequency of about 1.1 events per kilometer per year, similar to some other ice-scoured habitats in other polar regions. This rate may either increase or decrease with climate warming. Warmer temperatures may increase the rate of iceberg calving, increasing the supply of deep-keel ice structures. Alternately, warmer temperatures may reduce the thickness, strength, or movements of winter pack ice and associated scouring structures.
Monday, March 10, 2008
Hijmans et al. 2005
Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.
These authors describe the release of the WorldClim database, which includes data on several climate variables for a very large number of grid squares on land surfaces on Earth. Each grid square is 30 arc-seconds across, thus at the equator these squares are 0.816 square kilometers, and smaller (finer resolution) at higher latitudes.
Data for this database come primarily from weather stations located worldwide. Altitude was estimated from a Shuttle radar mission, for all latitudes south of 60°N, and excluding Antarctica. Each grid square’s climate was estimated by a complex interpolation algorithm that is analagous to regression: it fits a continuous surface to the points, but does not necessarily go through each point.
The authors describe some of the potential sources of error in the dataset, and urge higher quality data for future updates, for example by confirmation of precise locations for weather stations, and greater standardization in weather station record-keeping and reporting.
The database can be downloaded in a variety of formats from http://www.worldclim.org/. Most files are designed for use with GIS programs. A range of biologically meaningful data (maximum and minimum temperatures per year, seasonality) have been made available as well.
These authors describe the release of the WorldClim database, which includes data on several climate variables for a very large number of grid squares on land surfaces on Earth. Each grid square is 30 arc-seconds across, thus at the equator these squares are 0.816 square kilometers, and smaller (finer resolution) at higher latitudes.
Data for this database come primarily from weather stations located worldwide. Altitude was estimated from a Shuttle radar mission, for all latitudes south of 60°N, and excluding Antarctica. Each grid square’s climate was estimated by a complex interpolation algorithm that is analagous to regression: it fits a continuous surface to the points, but does not necessarily go through each point.
The authors describe some of the potential sources of error in the dataset, and urge higher quality data for future updates, for example by confirmation of precise locations for weather stations, and greater standardization in weather station record-keeping and reporting.
The database can be downloaded in a variety of formats from http://www.worldclim.org/. Most files are designed for use with GIS programs. A range of biologically meaningful data (maximum and minimum temperatures per year, seasonality) have been made available as well.
Friday, February 22, 2008
Just 1970
Just J. 1970. Amphipoda from Jørgen Brønlund fjord, north Greenland. Denmark, Kommissionen For Videnskabelige Undersøgelser I Grønland 184 (6): 39 pages.
This author describes the amphipods collected by two expeditions to north-east Greenland, including 28 species, one newly described. Many other species had not been previously reported from Greenland, or from north-east Greenland. Many specimens were collected from the stomach contents of Salvelinus alpinus, arctic char. Species identification is typically based on fine characteristics of the appendages, suggesting that even being consumed by a fish is not sufficient to immediately destroy an amphipod in some cases. Other specimens were collected from various depths, from 5 cm to deeper than 100 m in the fjord, using dredges and benthic grabs; one specimen was collected by hand from the shore.
I am unsure how to cite this work properly. It appears to be somewhere between a regular report (it has an apparent volume and issue number) and a monograph. I was able to check this out as a book from the University of Guelph library; I think I am the first person ever to do so, as I had to separate several pages that had not been properly separated when this work was printed and bound.
This author describes the amphipods collected by two expeditions to north-east Greenland, including 28 species, one newly described. Many other species had not been previously reported from Greenland, or from north-east Greenland. Many specimens were collected from the stomach contents of Salvelinus alpinus, arctic char. Species identification is typically based on fine characteristics of the appendages, suggesting that even being consumed by a fish is not sufficient to immediately destroy an amphipod in some cases. Other specimens were collected from various depths, from 5 cm to deeper than 100 m in the fjord, using dredges and benthic grabs; one specimen was collected by hand from the shore.
I am unsure how to cite this work properly. It appears to be somewhere between a regular report (it has an apparent volume and issue number) and a monograph. I was able to check this out as a book from the University of Guelph library; I think I am the first person ever to do so, as I had to separate several pages that had not been properly separated when this work was printed and bound.
Wednesday, January 16, 2008
Doležel et al. 1998
Doležel J, Greilhuber J, Lucretti S, Meister A, Lysák MA, Nardi L, Obermayer R. 1998. Plant genome size estimation by flow cytometry: Inter-laboratory comparison. Annals of Botany 82 (Supplement A): 17-26.
These authors compared pairwise ratios of measured genome sizes of nine species of plants covering a genome size range of 0.3-30pg, between four laboratories in central Europe (Austria, Czech Republic, Germany, Italy), using flow cytometry. The purpose of this “exercise” was to test the reliability and variability of flow cytometry for genome-size measurement in plants. Each lab used its own method of nuclei isolation and staining; one lab also measured these plant species using Feulgen densitometry. Two labs used laser-based flow cytometers, two used mercury arc-lamp-based flow cytometers. All labs used propidium iodide (PI), a DNA-intercalating agent that is not biased by sequence; one of each type of machine was also used with DAPI, which preferentially binds to AT-rich regions of chromosomes.
Their primary findings were 1. intra-lab variation was very low, 2. inter-lab variation was low but statistically significant (partly because intra-lab variation was so low), and 3. a consistent difference was found between mercury arc-lamp and laser-based flow cytometers. Additionally, they found that DAPI was not suitable for genome size estimation because of differences between plant species in GC contents. Variation in nuclei-isolating buffers did not have measureable effects on the results.
They make two key recommendations for future research into plant genome size variation using flow cytometry:
1. All samples should be analysed in one lab using one instrument. Replication of one lab’s findings by another should analyse whole sets of samples for reliable ratio comparisons.
2. Inter-lab and machine-type differences should be considered when evaluating published reports of genome size variation in plants.
Both of these recommendations underscore the need for detailed, clear Methods & Materials sections in scientific publications, including the need to identify staining protocols, instrument types, and similar fine details.
Finally, they urge a broad agreement on reference standards (i.e. species used as standards during measurement) and their calibration, to allow higher precision in estimated genome size variation among and within plant species.
These authors compared pairwise ratios of measured genome sizes of nine species of plants covering a genome size range of 0.3-30pg, between four laboratories in central Europe (Austria, Czech Republic, Germany, Italy), using flow cytometry. The purpose of this “exercise” was to test the reliability and variability of flow cytometry for genome-size measurement in plants. Each lab used its own method of nuclei isolation and staining; one lab also measured these plant species using Feulgen densitometry. Two labs used laser-based flow cytometers, two used mercury arc-lamp-based flow cytometers. All labs used propidium iodide (PI), a DNA-intercalating agent that is not biased by sequence; one of each type of machine was also used with DAPI, which preferentially binds to AT-rich regions of chromosomes.
Their primary findings were 1. intra-lab variation was very low, 2. inter-lab variation was low but statistically significant (partly because intra-lab variation was so low), and 3. a consistent difference was found between mercury arc-lamp and laser-based flow cytometers. Additionally, they found that DAPI was not suitable for genome size estimation because of differences between plant species in GC contents. Variation in nuclei-isolating buffers did not have measureable effects on the results.
They make two key recommendations for future research into plant genome size variation using flow cytometry:
1. All samples should be analysed in one lab using one instrument. Replication of one lab’s findings by another should analyse whole sets of samples for reliable ratio comparisons.
2. Inter-lab and machine-type differences should be considered when evaluating published reports of genome size variation in plants.
Both of these recommendations underscore the need for detailed, clear Methods & Materials sections in scientific publications, including the need to identify staining protocols, instrument types, and similar fine details.
Finally, they urge a broad agreement on reference standards (i.e. species used as standards during measurement) and their calibration, to allow higher precision in estimated genome size variation among and within plant species.
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