Hashimoto S, Suzuki M. 2002. Vertical distributions of carbon dioxide diffusion coefficients and production rates in forest soils. Soil Science Society of America Journal 66: 1151-1158.
These authors inverted the usual soil-gas measurement approach of inserting probes into soil: they inserted soil into their apparatus. “Undisturbed” soil samples approximately 20cm in diameter and 40cm long were collected from a research forest in Japan, dried for up to 17 days, and then placed into the laboratory apparatus. This consists of a sample cylinder big enough to take the soil samples, with chambers above and below that allow control of boundary conditions. Sample ports through the side of the cylinder allow measurement of CO2 concentrations at various positions in the sample. A set of pumps, valves, and tubes allow control of soil water conditions, including manipulation of water potential.
The point of this device is to measure CO2 diffusion in large soil samples, and control for water and temperature effects. Theories of soil gas diffusion can be tested using this apparatus.
Thursday, October 15, 2009
Kammann et al. 2001
Kammann C, Grünhage L, Jäger H-J. 2001. A new sampling technique to monitor concentrations of CH4, N2O and CO2 in air at well-defined depths in soils with varied water potential. European Journal of Soil Science 52: 297-303.
These authors invented a buried probe based on silicone tubing for long-term monitoring of soil gas concentrations. In essence, this is simply a length of silicone tubing coiled into a flat “snail” shape and secured with wire mesh, with silicone stoppers at both ends. One end is penetrated by a stainless steel tube that extends to the surface, and is topped with a stopcock that allows sampling by syringe. These authors tested their design in a few laboratory and field studies, and demonstrated the gases CH4, N2O and CO2 do indeed diffuse into the hollow interior of the probe, and reach 95% equilibration in as little as 7 hours. They state the advantages of their design over other soil gas probes, most notably the ability to use this design in very wet and saturated soils, which is where CH4 processes may be of greatest interest.
The downside of this probe design from my point of view is the need to dig a pit for these probes, and the consequent long wait before the disturbance has dissipated and accurate sampling can begin. However, for long-term monitoring of soil gas processes, particularly in wetlands and soils prone to heavy rainfall events, these probes appear to be very useful.
These authors invented a buried probe based on silicone tubing for long-term monitoring of soil gas concentrations. In essence, this is simply a length of silicone tubing coiled into a flat “snail” shape and secured with wire mesh, with silicone stoppers at both ends. One end is penetrated by a stainless steel tube that extends to the surface, and is topped with a stopcock that allows sampling by syringe. These authors tested their design in a few laboratory and field studies, and demonstrated the gases CH4, N2O and CO2 do indeed diffuse into the hollow interior of the probe, and reach 95% equilibration in as little as 7 hours. They state the advantages of their design over other soil gas probes, most notably the ability to use this design in very wet and saturated soils, which is where CH4 processes may be of greatest interest.
The downside of this probe design from my point of view is the need to dig a pit for these probes, and the consequent long wait before the disturbance has dissipated and accurate sampling can begin. However, for long-term monitoring of soil gas processes, particularly in wetlands and soils prone to heavy rainfall events, these probes appear to be very useful.
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.
Tuesday, October 6, 2009
Bohannan and Hughes 2003
Bohannan BJM, Hughes J. 2003. New approaches to analyzing microbial biodiversity data. Current Opinion in Microbiology. 6: 282-287.
These authors review the use of three broad approaches to studying microbial biodiversity in environments. The three are 1) parametric, 2) nonparametric, and 3) community phylogenetics. Each has advantages and disadvantages, and these authors suggest a combined approach may be most beneficial. Both 1) and 2) are based on Operational Taxonomic Units, to avoid the many problems of bacterial species identification, while 3) is based on molecular phylogenies, typically 16s rDNA.
Parametric approaches make simplifying assumptions and are based on some model of species richness in microbial communities; often this model is log-normal, in which some taxa are rare, some are abundant, and most are intermediate. These approaches extrapolate from patterns in a sample to the total environment. The obvious downside to parametric approaches is the vulnerability of the model to incorrect and difficult to test assumptions.
Nonparametric approaches avoid assuming any model, and instead are typically built on an approach analogous to mark-release-recapture. Sequences encountered more than once in a sample are recaptures, and the frequency of these doubletons is assumed to be related to how many unique sequences are present: more doubletons means fewer total sequences. As a downside, these approaches provide only a lower limit to actual richness, thus generally underestimating total diversity.
Community phylogenetics approaches avoid the OTU concept and thereby preserve useful data in the form of genetic information about sequences and sequence relationships. The downside of community phylogenetics approaches is they sample a clone library derived from the environment, not the environment directly, and can therefore not extrapolate from the sample to the environment.
This paper provides several useful examples of each approach, and supports the utility of Martin’s (2002) combined approach, which is what I would like to apply to my data to be collected in 2010. Figure 3 in this paper, for example, provides a useful overview of what Martin (2002) did, and how to make inferences about observed patterns.
These authors review the use of three broad approaches to studying microbial biodiversity in environments. The three are 1) parametric, 2) nonparametric, and 3) community phylogenetics. Each has advantages and disadvantages, and these authors suggest a combined approach may be most beneficial. Both 1) and 2) are based on Operational Taxonomic Units, to avoid the many problems of bacterial species identification, while 3) is based on molecular phylogenies, typically 16s rDNA.
Parametric approaches make simplifying assumptions and are based on some model of species richness in microbial communities; often this model is log-normal, in which some taxa are rare, some are abundant, and most are intermediate. These approaches extrapolate from patterns in a sample to the total environment. The obvious downside to parametric approaches is the vulnerability of the model to incorrect and difficult to test assumptions.
Nonparametric approaches avoid assuming any model, and instead are typically built on an approach analogous to mark-release-recapture. Sequences encountered more than once in a sample are recaptures, and the frequency of these doubletons is assumed to be related to how many unique sequences are present: more doubletons means fewer total sequences. As a downside, these approaches provide only a lower limit to actual richness, thus generally underestimating total diversity.
Community phylogenetics approaches avoid the OTU concept and thereby preserve useful data in the form of genetic information about sequences and sequence relationships. The downside of community phylogenetics approaches is they sample a clone library derived from the environment, not the environment directly, and can therefore not extrapolate from the sample to the environment.
This paper provides several useful examples of each approach, and supports the utility of Martin’s (2002) combined approach, which is what I would like to apply to my data to be collected in 2010. Figure 3 in this paper, for example, provides a useful overview of what Martin (2002) did, and how to make inferences about observed patterns.
Fang and Moncrieff 1998
Fang C, Moncrieff JB. 1998. Simple and fast technique to measure CO2 profiles in soil. Soil Biology and Biochemistry 30: 2107-2112.
These authors present a method they developed to measure sub-surface CO2 concentrations in soil. Their test environment was a slash pine (Pinus elliotti) plantation in Florida, with sandy soil subject to a broadly fluctuating water table that occasionally comes to the surface.
Their method, essentially, involves burying a perforated aluminum probe connected to the surface with flexible tubing, waiting several weeks for the disturbance to settle, and then measuring recirculated gas samples by injecting them with a syringe into an IRGA. Recirculation breaks the trade-off between errors associated with the syringe sucking air out of surrounding soils at depths different from the intended sample, and large buffer volumes inside probes become dead spaces with internal gas concentration gradients.
This is an interesting approach to soil gas probes, but is fundamentally unsuitable for my own studies because of the necessity of waiting weeks before sampling due to the disturbance of burying the probes.
These authors present a method they developed to measure sub-surface CO2 concentrations in soil. Their test environment was a slash pine (Pinus elliotti) plantation in Florida, with sandy soil subject to a broadly fluctuating water table that occasionally comes to the surface.
Their method, essentially, involves burying a perforated aluminum probe connected to the surface with flexible tubing, waiting several weeks for the disturbance to settle, and then measuring recirculated gas samples by injecting them with a syringe into an IRGA. Recirculation breaks the trade-off between errors associated with the syringe sucking air out of surrounding soils at depths different from the intended sample, and large buffer volumes inside probes become dead spaces with internal gas concentration gradients.
This is an interesting approach to soil gas probes, but is fundamentally unsuitable for my own studies because of the necessity of waiting weeks before sampling due to the disturbance of burying the probes.
Cockell and Stokes 2004
Cockell CS, Stokes MD. 2004. Widespread colonization by polar hypoliths. Nature 431: 414.
These authors present a short report about the colonization of the undersides of rocks in the polar deserts by cyanobacteria and unicellular green algae. Where rocks have a protected but accessible underside, these organisms colonize, forming a pale green band a few centimetres across, between the part of the rock too exposed and dry, and too dark for photosynthesis. In polygon terrain, where the ground is sorted by frost heave (“periglacial processes”) and even large rocks are periodically jostled, areas of finer texture form in the centers of polygons, with larger rocks around the edges. The edge rocks were 100% colonized, while central areas were 5% colonized.
These authors present a short report about the colonization of the undersides of rocks in the polar deserts by cyanobacteria and unicellular green algae. Where rocks have a protected but accessible underside, these organisms colonize, forming a pale green band a few centimetres across, between the part of the rock too exposed and dry, and too dark for photosynthesis. In polygon terrain, where the ground is sorted by frost heave (“periglacial processes”) and even large rocks are periodically jostled, areas of finer texture form in the centers of polygons, with larger rocks around the edges. The edge rocks were 100% colonized, while central areas were 5% colonized.
Fierer and Jackson 2006
Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the U.S.A. 103: 626-631.
These authors measured biodiversity of soil bacterial communities from 98 samples across North and South America. Rather than the expected variables that structure macroorganism biodiversity such as climate and latitude, the single most important factor for bacterial community diversity was soil pH. Soils with higher pH had greater biodiversity, regardless of geographic separation between sites or geographic position. Because soils with pH greater than 8.5 are rare, it is impossible to distinguish between a unimodal distribution, and a plateau at near-neutral pH.
Most surprising to me was the lack of correlation between bacterial diversity, as either species richness or Shannon-index diversity (richness and evenness) and plant diversity. While these authors did not assess plant diversity, they did express their own surprise that sites in the Peruvian Amazon, with acidic soils, had very low bacterial diversity despite having one of the highest measured plant biodiversities on Earth, and expanded their soil collecting sites to include other tropical and sub-tropical forests with very high plant diversity. Sites with near-neutral pH provided the highest estimates of bacterial diversity, and were primarily dry-grassland, dry-forest, and humid temperate forest sites, with low-to-intermediate plant diversity.
The method used to estimate diversity of bacterial communities was terminal-restriction fragment length polymorphism analysis, or T-RFLP. This technique relies on PCR to amplify the sequence of interest, in this case 16S rDNA, followed by digestion with restriction endonucleases and generation of “fingerprints” for each community. This is a fairly low-resolution method, with less than 100 bands per community, and no ability to distinguish between species with similar restriction sites. However, it does permit high throughput and costs much less per sample than does cloning and sequencing.
This paper is an excellent example of a recent study supporting the hypothesis that microbial global biodiversity is controlled by factors quite distinct from the factors controlling macroorganism (plant and animal) biodiversity. In this case, soil pH is the master control variable, rather than climate or climate factors.
These authors measured biodiversity of soil bacterial communities from 98 samples across North and South America. Rather than the expected variables that structure macroorganism biodiversity such as climate and latitude, the single most important factor for bacterial community diversity was soil pH. Soils with higher pH had greater biodiversity, regardless of geographic separation between sites or geographic position. Because soils with pH greater than 8.5 are rare, it is impossible to distinguish between a unimodal distribution, and a plateau at near-neutral pH.
Most surprising to me was the lack of correlation between bacterial diversity, as either species richness or Shannon-index diversity (richness and evenness) and plant diversity. While these authors did not assess plant diversity, they did express their own surprise that sites in the Peruvian Amazon, with acidic soils, had very low bacterial diversity despite having one of the highest measured plant biodiversities on Earth, and expanded their soil collecting sites to include other tropical and sub-tropical forests with very high plant diversity. Sites with near-neutral pH provided the highest estimates of bacterial diversity, and were primarily dry-grassland, dry-forest, and humid temperate forest sites, with low-to-intermediate plant diversity.
The method used to estimate diversity of bacterial communities was terminal-restriction fragment length polymorphism analysis, or T-RFLP. This technique relies on PCR to amplify the sequence of interest, in this case 16S rDNA, followed by digestion with restriction endonucleases and generation of “fingerprints” for each community. This is a fairly low-resolution method, with less than 100 bands per community, and no ability to distinguish between species with similar restriction sites. However, it does permit high throughput and costs much less per sample than does cloning and sequencing.
This paper is an excellent example of a recent study supporting the hypothesis that microbial global biodiversity is controlled by factors quite distinct from the factors controlling macroorganism (plant and animal) biodiversity. In this case, soil pH is the master control variable, rather than climate or climate factors.
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