Progress 08/01/08 to 07/31/12
Outputs
OUTPUTS: The overarching objective of this proposal is to understand how microbial communities respond to soil moisture variability. Our efforts have focused on the following activities: 1) computer simulations of bacteria in soil habitats undergoing fluctuations in water and soil properties to assess how physics and traits influence microbial diversity, 2) ecophysiological experiments with bacterial and fungal isolates to determine whether there is a phylogenetic signal associated with the moisture niche of soil microbes, 3) stable isotope probing (SIP) to determine which bacteria respond to soil rewetting and contribute to pulses of ecosystem activity across a land-use gradient, 4) field experiments using sensor technology to determine how precipitation variability (snow and rain) alter the sensitivity of microbial respiration and community structure. PARTICIPANTS: Jay T. Lennon (PD, MSU), Zach Aanderud (Co-PD, Brigham Young University), Chris Klausmeier (Co-PD, MSU), Brent Lehmkuhl (Research Technician, MSU), Donald Schoolmaster (Collaborator, MSU), Noah Fierer (Collaborator, University of Colorado), Stuart Jones (Collaborator, Notre Dame University), Sarah Placella (Michigan State University) TARGET AUDIENCES: Results from this proposal will be targeted primarily towards the academic audience. We have also made efforts to disseminate our results to local and state agencies interested in soil properties. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Activity 1: We have created an individual-based cellular automaton model that simulates microbial species interactions in a heterogeneous soil matrix. The model allows us to manipulate soil texture, including the composition of sand, clay, and pore space. We are then able to introduce microbial species into the simulation, which have different physiological tolerances to moisture levels and different functional traits. Last, we can manipulate the timing and amount of moisture in the simulations to explore the interactions between precipitation regimes, soil properties, and physiological traits on the coexistence of soil microorganisms. Activity 2: We have characterized the physiological response curves of ~50 different microbial (bacterial and fungi) strains. Many of these strains were isolated from the Kellogg Biological Station (KBS). These strains were purified, sequenced, and are now stored at -80C. We measured CO2 production along a water potential gradient for all strains. From this, we quantified three important niche parameters: niche breadth, maximum respiration, and tolerance to desiccation. Using randomization procedures, we have been able to determine that these niche parameters are phylogenetically conserved at a fairly broad taxonomic level (phylum) and are correlated with a strains ability to produce biofilms. Activity 3: We have developed and refined a method for using heavy water (H218O) in combination with stable isotope probing (SIP). Using LC-MS, we have tracked the incorporation of 18O into thymidine monophosphate, including the phosphate backbone, deoxyribose sugar, and the thymine nucleobase. We then used the technique to identify bacteria across a land-use gradient that respond to rewetting. We characterized the bacteria using tag 16S pyrosequencing. From this, we have identified bacteria that are associated with pulsed ecosystem activity, and discovered that many of the rare taxa in soils are metabolically active and important for generating CO2 pulses. Activity 4: we performed field-scale precipitation manipulations on the KBS-LTER in both successional grasslands and deciduous forest. We deployed high-resolution sensors that tracked changes in temperature, moisture, and CO2. Precipitation variability altered the ways in which microbial respiration responds to environmental drivers (i.e., temperature and moisture). These affects correspond with changes in microbial structure, but seasonal transitions appear to "reset" communities suggesting that microbial communities may be resilient to some global change stressors such as altered precipitation.
Publications
- Fierer N, Lennon JT (2011) The generation and maintenance of diversity in microbial communities. American Journal of Botany 98: 439-448.
- Shade A, Peter H, Allison SD, Baho D, Berga M, Burgman H, Handelsman J, Huber D, Langender S, Lennon JT, Martiny J, Matulich K, Schmidt TM. (2012) Microbial community stability: resistance and resilience. In Review.
- Lau JA, Lennon JT (2012) Rapid responses of soil microorganisms improve plant fitness in novel environments. Proceedings of the National Academy of Sciences of the United States of America 109: 14058-14062.
- Lennon JT, Jones SE (2011) Microbial seed banks: ecological and evolutionary implications of dormancy. Nature Reviews Microbiology 9:119-130.
- Lennon JT (2011) Replication, lies, and lesser-known truths regarding experimental design in environmental microbiology. Environmental Microbiology 6:1383-1386.
- Aanderud ZA, Jones SE, Schoolmaster DR, Fierer N. Lennon JT (2012) Sensitivity of soil respiration and microbial communities to altered snowfall. Soil Biology & Biochemistry (In Press).
- Lennon JT, Aanderud ZA, Lehmkuhl BK, Schoolmaster DR (2012) Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology 93: 1867-1879.
- Treseder KK, Balser TC, Bradford MA, Brodie EL, Eviner VT, Hofmockel KS, Lennon JT, Levine UY, MacGregor BJ, Pett-Ridge J, Waldrop MP (2012) Integrating microbial ecology into ecosystem models. Biogeochemistry 109: 7-18.
- Jones SE, Lennon JT (2010) Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences of the United States of America 107: 5881-5886.
- Lau JA, Lennon JT (2011) Evolutionary ecology of plant-microbe interactions: soil microbial structure alters natural selection on plant traits. New Phytologist 192:215-224.
- Aanderud ZT, Lennon JT (2011) Validation of heavy-water stable isotope probing for the characterization of rapidly responding soil bacteria. Applied and Environmental Microbiology 77: 4589-4596.
- Aanderud ZT, Schoolmaster DR, Lennon JT (2011) Plants mediate the sensitivity of soil respiration to rainfall variability. Ecosystems 14: 156-167.
- Jones SE, Lennon JT (2010) Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences of the United States of America 107: 5881-5886.
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Progress 08/01/10 to 07/31/11
Outputs
OUTPUTS: The overarching objective of this proposal is to understand how microbial communities respond to soil moisture variability. Our efforts have focused on the following activities: 1) computer simulations of bacteria in soil habitats undergoing fluctuations in water and soil properties to assess how physics and traits influence microbial diversity, 2) ecophysiological experiments with bacterial and fungal isolates to determine whether there is a phylogenetic signal associated with the moisture niche of soil microbes, and 3) stable isotope probing (SIP) to determine which bacteria respond to soil rewetting and contribute to pulses of ecosystem activity across a land-use gradient. PARTICIPANTS: Jay T. Lennon (PD, MSU), Zach Aanderud (Co-PD, Brigham Young University), Chris Klausmeier (Co-PD, MSU), Brent Lehmkuhl (Research Technician, MSU), Donald Schoolmaster (Collaborator, MSU), Noah Fierer (Collaborator, University of Colorado), Stuart Jones (Collaborator, Notre Dame University), Sarah Placella (Michigan State University), Noah Fierer (University of Colorado) TARGET AUDIENCES: Results from this proposal will be targeted primarily towards the academic audience. We will also make an effort to disseminate our results to local and state agencies interested in soil properties. Some of our research may also dovetail with a recently funded DOE Bioenergy proposal, which has significant extension opportunities. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Activity 1: We have created an individual-based cellular automaton model that simulates microbial species interactions in a heterogeneous soil matrix. The model allows us to manipulate soil texture, including the composition of sand, clay, and pore space. We are then able to introduce microbial species into the simulation, which have different physiological tolerances to moisture levels and different functional traits. Last, we can manipulate the timing and amount of moisture in the simulations to explore the interactions between precipitation regimes, soil properties, and physiological traits on the coexistence of soil microorganisms. We have recently hired a new postdoc, Dr. Sarah Placella, who is working on the simulations. Activity 2: We have characterized the physiological response curves of ~50 different microbial strains. Many of these strains were isolated from the Kellogg Biological Station (KBS). These strains were purified, sequenced, and are now stored at -80C. We measured CO2 production along a water potential gradient for all 50 strains. From this, we quantified three important niche parameters: niche breadth, maximum respiration, and tolerance to desiccation. Using randomization procedures, we have been able to determine that these niche parameters are phylogenetically conserved at a fairly broad taxonomic level (phylum) and are correlated with a strains ability to produce biofilms. Activity 3: We have developed and refined a method for using heavy water (H218O) in combination with stable isotope probing (SIP). Using LC-MS, we have tracked the incorporation of 18O into thymidine monophosphate, including the phosphate backbone, deoxyribose sugar, and the thymine nucleobase. We then used the technique to identify bacteria across a land-use gradient that respond to rewetting. We characterized the bacteria using tag 16S pyrosequencing. From this, we have identified bacteria that are associated with pulsed ecosystem activity, and discovered that many of the rare taxa in soils are metabolically active and important for generating CO2 pulses.
Publications
- Aanderud ZT, Jones SE, Schoolmaster DR, Fierer N, Lennon JT. (2011) Sensitivity of soil respiration and microbial communities to altered snowfall. In Review.
- Lau JA, Lennon JT. (2011) Evolutionary ecology of plant-microbe interactions: soil microbial structure alters natural selection on plant traits. New Phytologist. 192: 215-224.
- Tresder KK, Balser TC, Bradford MA, Brodie EL, Eviner VT, Hofmockel KS, Lennon JT, Levine UY, MacGregor BJ, Pett-Ridge J, Waldrop MP. (2011) Integrating microbial ecology into ecosystem models. Biogeochemistry. DOI 10.1007/s10533-011-9636-5
- Aanderud ZT, Lennon JT. (2011) Validation of heavy-water stable isotope probing for the characterization of rapid responding soil bacteria. Applied and Environmental Microbiology. 13: 4589-4596
- Lennon JT, Jones SE (2011) Microbial seed banks: ecological and evolutionary implications of dormancy. Nature Reviews Microbiology 9:119-130
- Lennon JT (2011) Replication, lies, and lesser-known truths regarding experimental design in environmental microbiology. Environmental Microbiology. 13: 1383-1386.
- Fierer N, Lennon JT (2011) The generation and maintenance of diversity in microbial communities. American Journal of Botany. 98: 439-448.
- Aanderud ZT, Schoolmaster DR, Lennon JT (2011) Plants mediate the sensitivity of soil respiration to rainfall variability. Ecosystems. 14: 156-167.
- Lennon JT, Aanderud ZA, Lehmkuhl BK, Schoolmaster DR. (2011) Mapping the niche space of soil microorganisms using taxonomy and traits. In Review.
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Progress 08/01/09 to 07/31/10
Outputs
OUTPUTS: The overarching objective of this proposal is to understand how microbial communities respond to soil moisture variability. Our efforts have focused on the following activities: 1) We are conducting computer simulations of bacteria in soil habitats undergoing fluctuations in water and soil properties to assess how moisture influences microbial diversity, 2) we are conducting ecophysiological experiments with bacterial and fungal isolates to determine whether there is a phylogenetic signal associated with the moisture niche of soil microbes, and 3) we are using stable isotope probing (SIP) to determine which bacteria actively respond to soil rewetting and contribute to pulses of ecosystem activity across a land-use gradient. PARTICIPANTS: Jay T. Lennon (PD, MSU), Zach Aanderud (Co-PD, Brigham Young University), Chris Klausmeier (Co-PD, MSU), Brent Lehmkuhl (Research Technician, MSU), Donald Schoolmaster (Collaborator, MSU), Noah Fierer (Collaborator, University of Colorado), Stuart Jones (Collaborator, Notre Dame University). TARGET AUDIENCES: Results from this proposal will be targeted primarily towards the academic audience. We will also make an effort to disseminate our results to local and state agencies interested in soil properties. Some of our research may also dovetail with a recently funded DOE Bioenergy proposal, which has significant extension opportunities. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Activity 1: We have created an individual-based cellular automaton model that simulates microbial species interactions in a heterogeneous soil matrix. The model allows us to manipulated soil texture, including the composition of sand, clay, and pore space. We are then able to introduce microbial species into the simulation, which have different physiological tolerances to moisture levels. Lastly, we can manipulate the timing and amount of moisture in the simulations to explore the interactions between precipitation regimes, soil properties, and physiological traits on the coexistence of soil microorganisms. We have recently hired a new postdoc who will be working on the next stages of the simulations. Activity 2: We have characterized the physiological response curves of ~50 different microbial strains. Many of these strains were isolated from the Kellogg Biological Station (KBS). These strains were purified, sequenced, and are now stored at -80C. We measured CO2 production along a water potential gradient for all 50 strains. From this, we quantified three important niche parameters: niche breadth, maximum respiration, and tolerance to desiccation. Using randomization procedures, we have been able to determine that these niche parameters are phylogenetically conserved at a fairly broad taxonomic level and are correlated with a strains ability to produce biofilms. Activity 3: We have developed and refined a method for using heavy water (H218O) in combination with stable isotope probing (SIP). Using LC-MS, we have tracked the incorporation of 18O into thymidine monophosphate, including the phosphate backbone, deoxyribose sugar, and the thymine nucleobase. We then used the technique to identify bacteria across a land-use gradient that respond to rewetting. We characterized the bacteria using tag 16S pyrosequencing. From this, we have identified bacteria that are associated with pulsed ecosystem activity, and discovered that many of the rare taxa in soils are metabolically active and important for generating CO2 pulses.
Publications
- No publications reported this period
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Progress 08/01/08 to 07/31/09
Outputs
OUTPUTS: The overarching objective of this proposal is to understand how microbial communities and ecosystem processes change in response to precipitation variability. Activities: 1) Microbial community responses to precipitation variability. We are using a stable isotope probing technique (SIP) that uses heavy water (H218O) to identify soil bacteria that are metabolically active following precipitation events. We have successfully extracted isotopically labeled DNA and RNA from both pure cultures of bacteria and from soil samples in different land use treatments at the Kellogg Biological Station's (KBS) Long Term Ecology Research site. Over the past year, we have been developing and refining SIP procedures at KBS using a recently purchased benchtop ultracentrifuge, fraction collector, and quantitative PCR (qPCR) machine. Moreover, we have been conducting experiments to understand how isotopically labeled water is incorporated into microbial nucleic acids to ensure that our assumptions about using SIP to make inferences about the composition of metabolically active soil bacteria are robust. 2) Ecosystem responses to precipitation variability. We have developed and applied real-time sensor technology to measure soil responses to natural and manipulated precipitation variability. We are using CO2, soil moisture, and temperature sensors. These sensors are deployed in different land use treatments at KBS and are configured to transfer data wirelessly to our laboratory for monitoring and analysis. We have made significant progress with the analysis of our sensor data using a combination of time series regression and maximum likelihood analysis, which should be useful for other scientists that are generating large data sets with sensor technology. PARTICIPANTS: Jay T. Lennon - PI, Michigan State University, Kellogg Biological Station; Zach Aanderud - Postdoc, Michigan State University, Kellogg Biological Station; Brent Lehmkuhl - Research Technician, Michigan State University, Kellogg Biological Station; Cathy McMinn - Research; Technician, Michigan State University, Kellogg Biological Station; Ben Phillips - Undergraduate Research Technician, Michigan State University, Kellogg Biological Station; Taiquitha Robins - Undergraduate Research Technician, Michigan State University, Kellogg Biological Station; Donald Schoolmaster - Collaborator, State University, Kellogg Biological Station; Kali Bird - Graduate Rotation student; Ben Roller - Graduate Rotation student; Ben Koestler - Graduate Rotation student; Nicholas Flugga - Graduate Rotation student; Stuart Jones - Postdoc, Michigan State University, Kellogg Biological Station; Evan Kane - Postdoc, Michigan State University, Kellogg Biological Station TARGET AUDIENCES: Results from this proposal will be targeted primarily towards the academic audience. We will also make an effort to disseminate our results to local and state agencies interested in soil properties. Some of our research may also dovetail with a recently funded DOE Bioenergy proposal, which has significant extension opportunities. PROJECT MODIFICATIONS: No notable modifications have been made to the project
Impacts
1) Microbial community responses to precipitation variability. We are still in the process of generating results pertaining to the metabolic activity of soil bacteria in response to precipitation variability. We have recently optimized the stable isotope probing (SIP) procedure and have generated some data using 454 pyrosequencing technology. We are currently in the process of analyzing these data. In addition, we have been exploring the mechanisms of heavy water incorporation into the nucleic acids of microbial taxa using a combination of qPCR and nuclear magnetic resonance (NMR). This is important because it will test whether there are artifacts with the heavy-water SIP approach that would weaken our microbial inference space. 2) Ecosystem responses to precipitation variability. We have generated and analyzed data from field experiments that address how plant mediate CO2 responses to precipitation variability. Our field scale manipulation documented how plant removal in different land use treatments affected soil moisture, temperature, nitrogen, carbon, methane and nitrous oxide flux. On top of this experimental template we documented significant changes in CO2 responses to investigator-imposed precipitation regimes. Our results suggest that plant communities have the ability to dampen fluctuation in soil moisture and thus reduce the amount and variability of CO2 flux from Midwestern agricultural landscapes.
Publications
- No publications reported this period
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