Rich Lab:Research

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 2: Line 2:
-
<font color=blue> '''Carbon cycling in thawing permafrost ecosystems''' <br>
+
<font color=blue> <big><big>'''Carbon cycling in thawing permafrost ecosystems''' </big></big><br>
<font color=black>Permafrost stores ~a third of the world’s soil organic carbon, in a relatively inaccessible frozen form. Under continued climate warming, permafrost is projected to decrease 50% by 2050 and be virtually eliminated by century’s end. Thawed permafrost frequently becomes wetland, which is a major source of the potent greenhouse gas methane, thereby raising the potential for dramatic positive feedbacks to warming. Our interdisciplinary DOE-funded project (renewed in 2013) examines the effects of natural ''in situ'' permafrost thaw on carbon cycling, by examining an existing permafrost thaw gradient in subarctic Sweden. We are focusing high-resolution, cutting-edge microbial and biogeochemical investigations across the three habitats defining this gradient: intact permafrost, intermediate-thaw peat bog, and fully-thawed fen wetland. Our results are being integrated into a wetland ecosystem process model that predicts greenhouse gas emissions, and the lessons generalized for inclusion in global climate models (which do not include or poorly characterize permafrost thaw). SWES-MEL co-leads this work and is one of two microbial ecology labs on the project, and our focus is on molecular analyses of microbial community composition and activity (16S rRNA gene surveys, metagenomics, and metaproteomics). Through this work, we hope to address how permafrost thaw effects carbon cycling, predict the likelihood and magnitude of global warming feedbacks, and add a mechanistic framework for scaling from “genes to ecosystems” in this biome.  <br>
<font color=black>Permafrost stores ~a third of the world’s soil organic carbon, in a relatively inaccessible frozen form. Under continued climate warming, permafrost is projected to decrease 50% by 2050 and be virtually eliminated by century’s end. Thawed permafrost frequently becomes wetland, which is a major source of the potent greenhouse gas methane, thereby raising the potential for dramatic positive feedbacks to warming. Our interdisciplinary DOE-funded project (renewed in 2013) examines the effects of natural ''in situ'' permafrost thaw on carbon cycling, by examining an existing permafrost thaw gradient in subarctic Sweden. We are focusing high-resolution, cutting-edge microbial and biogeochemical investigations across the three habitats defining this gradient: intact permafrost, intermediate-thaw peat bog, and fully-thawed fen wetland. Our results are being integrated into a wetland ecosystem process model that predicts greenhouse gas emissions, and the lessons generalized for inclusion in global climate models (which do not include or poorly characterize permafrost thaw). SWES-MEL co-leads this work and is one of two microbial ecology labs on the project, and our focus is on molecular analyses of microbial community composition and activity (16S rRNA gene surveys, metagenomics, and metaproteomics). Through this work, we hope to address how permafrost thaw effects carbon cycling, predict the likelihood and magnitude of global warming feedbacks, and add a mechanistic framework for scaling from “genes to ecosystems” in this biome.  <br>
* ''SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones, Gary Trubl, Moira Hough, Darya Anderson, Akos Owusu-Dommey, Morgan Binder, Maya Sederholm, Krystalle Diaz''<br>
* ''SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones, Gary Trubl, Moira Hough, Darya Anderson, Akos Owusu-Dommey, Morgan Binder, Maya Sederholm, Krystalle Diaz''<br>
Line 8: Line 8:
''
''
   
   
-
<font color=blue>'''Microbiology in the Critical Zone: geomicrobiology, "hot spots and hot moments", and ecosystem services in the Jemez River Basin – Santa Catalina Mountains Critical Zone Observatory
+
<font color=blue><big><big>'''Microbiology in the Critical Zone: geomicrobiology, "hot spots and hot moments", and ecosystem services in the JRB-SCM CZO
-
'''<br><font color=black>
+
'''</big></big><br><font color=black>
Together with the University of Arizona lab of Dr. Rachel Gallery, our lab has recently begun microbial investigations within the Jemez River Basin – Santa Catalina Mountains Critical Zone Observatory ([http://criticalzone.org/jemez-catalina/ JRB-SCM CZO]).  This CZO, led by [http://swes.cals.arizona.edu/chorover_lab/Home.html Jon Chorover], has developed a conceptual framework of (a) “hot spots and hot moments”, where landscape change occurs non-uniformly over space and time, for example occurring rapidly after major fire events (which our CZO just experienced in summer 2013), and (b) an energy/carbon flow equation ("EEMT", effective energy and mass transfer, developed by CZO PI [http://swes.cals.arizona.edu/rasmussen/ Craig Rasmussen]) that quantitatively describes critical zone landscape evolution. With the CZO renewal in summer 2013 (and a new inclusion of CZ ecosystem services in the research mission), our lab and the Gallery Lab have begun to bridge microbiology and CZO biogeochemistry in the context of water and soil processes, including decomposition, weathering, carbon stabilization, and carbon flow, and water purification. Our approach spans both physiological (Gallery Lab) and meta-omic (our lab) approaches.  
Together with the University of Arizona lab of Dr. Rachel Gallery, our lab has recently begun microbial investigations within the Jemez River Basin – Santa Catalina Mountains Critical Zone Observatory ([http://criticalzone.org/jemez-catalina/ JRB-SCM CZO]).  This CZO, led by [http://swes.cals.arizona.edu/chorover_lab/Home.html Jon Chorover], has developed a conceptual framework of (a) “hot spots and hot moments”, where landscape change occurs non-uniformly over space and time, for example occurring rapidly after major fire events (which our CZO just experienced in summer 2013), and (b) an energy/carbon flow equation ("EEMT", effective energy and mass transfer, developed by CZO PI [http://swes.cals.arizona.edu/rasmussen/ Craig Rasmussen]) that quantitatively describes critical zone landscape evolution. With the CZO renewal in summer 2013 (and a new inclusion of CZ ecosystem services in the research mission), our lab and the Gallery Lab have begun to bridge microbiology and CZO biogeochemistry in the context of water and soil processes, including decomposition, weathering, carbon stabilization, and carbon flow, and water purification. Our approach spans both physiological (Gallery Lab) and meta-omic (our lab) approaches.  
* ''SWES-MEL scientist involved: Robert Jones, Gayle Frost'' <br>
* ''SWES-MEL scientist involved: Robert Jones, Gayle Frost'' <br>
Line 15: Line 15:
''
''
-
<font color=blue>'''The Great Barrier Reef "Microbial Buffering" Project
+
<font color=blue><big><big>'''The Great Barrier Reef "Microbial Buffering" Project
-
'''<br><font color=black>
+
'''</big></big><br><font color=black>
One of the threats to global reef systems in general, including the Great Barrier Reef, is coastal pollution. In northeastern Australia extensive land-use change to agriculture over the last century has brought coastal pollution from herbicides, pesticides, nutrients, and organic matter.  Our collaborator Gene Tyson put forth the hypothesis that coastal microbial and viral communities may "buffer" reefs from the full impacts of pollution by taking up and/or transforming contaminants, and he, Matt Sullivan and myself developed a project to test this hypothesis. We partnered with David Bourne and Britta Schaffelke of the Australian Institute of Marine Science, who run extensive existing monitoring programs of coastal water quality and reef health, so that we could layer microbial and viral investigations on top of this rich and highly relevant metadata.<br>
One of the threats to global reef systems in general, including the Great Barrier Reef, is coastal pollution. In northeastern Australia extensive land-use change to agriculture over the last century has brought coastal pollution from herbicides, pesticides, nutrients, and organic matter.  Our collaborator Gene Tyson put forth the hypothesis that coastal microbial and viral communities may "buffer" reefs from the full impacts of pollution by taking up and/or transforming contaminants, and he, Matt Sullivan and myself developed a project to test this hypothesis. We partnered with David Bourne and Britta Schaffelke of the Australian Institute of Marine Science, who run extensive existing monitoring programs of coastal water quality and reef health, so that we could layer microbial and viral investigations on top of this rich and highly relevant metadata.<br>
* ''SWES-MEL scientist involved: Lynn Massey'' <br>
* ''SWES-MEL scientist involved: Lynn Massey'' <br>
Line 22: Line 22:
''
''
-
<font color=blue>'''Understanding the system response of soil to compost additions, in partnership with the UA Land Stewardship Program
+
<font color=blue><big><big>'''Understanding the system response of soil to compost additions, in partnership with the UA Land Stewardship Program
-
'''<br><font color=black>
+
'''</big></big><br><font color=black>
Turf grass covers more land area in the US than any agricultural crop, and has a higher chemical input than any agricultural crop. Managing it sustainably is key to minimizing its long-term impacts on water supply and watershed and atmosphere quality. The UA Land Stewardship Program has converted the management of the UA Mall’s turf grass from conventional to organic practices, after trials demonstrated that treating UA turfgrass with compost tea resulted in a range of system improvements, including decreased water use, increased C sequestration, deeper root depth, and the almost complete replacement of root-feeding nematodes by beneficial species (Pew and Hollar, 2011). Remarkably, compost tea application has also been shown to directly stimulate some plant “immune system” response, with increased protection from soil microbial and fungal pathogens; this response may be due to the direct physical interaction of compost-delivered microbes and plant root border cells (Curlango-Rivera, submitted). Reduction in fertilization should also reduce turf grass emissions of the greenhouse gas N2O, since its fluxes are strongly coupled to excess nitrogen related to fertilizer additions (Townsend-Small and Czimczik, 2010), however the full picture of compost effects on greenhouse gas emissions has not been performed. SWES-MEL is co-leading a team of UA researchers in a wholistic assessment of how compost treatments impact the soil community ecosystem and in turn influence greenhouse gas balance. Soil microorganisms are responsible for most below-ground carbon and nitrogen cycling, and therefore greenhouse has cycling, and so our lab’s research on the microbial communities is central to understanding ecosystem response. This research will allow turfgrass managers to make more informed decisions about their management practices, and will also be relevant to sustainable management decisions using compost treatments on diverse agricultural crops.<br>
Turf grass covers more land area in the US than any agricultural crop, and has a higher chemical input than any agricultural crop. Managing it sustainably is key to minimizing its long-term impacts on water supply and watershed and atmosphere quality. The UA Land Stewardship Program has converted the management of the UA Mall’s turf grass from conventional to organic practices, after trials demonstrated that treating UA turfgrass with compost tea resulted in a range of system improvements, including decreased water use, increased C sequestration, deeper root depth, and the almost complete replacement of root-feeding nematodes by beneficial species (Pew and Hollar, 2011). Remarkably, compost tea application has also been shown to directly stimulate some plant “immune system” response, with increased protection from soil microbial and fungal pathogens; this response may be due to the direct physical interaction of compost-delivered microbes and plant root border cells (Curlango-Rivera, submitted). Reduction in fertilization should also reduce turf grass emissions of the greenhouse gas N2O, since its fluxes are strongly coupled to excess nitrogen related to fertilizer additions (Townsend-Small and Czimczik, 2010), however the full picture of compost effects on greenhouse gas emissions has not been performed. SWES-MEL is co-leading a team of UA researchers in a wholistic assessment of how compost treatments impact the soil community ecosystem and in turn influence greenhouse gas balance. Soil microorganisms are responsible for most below-ground carbon and nitrogen cycling, and therefore greenhouse has cycling, and so our lab’s research on the microbial communities is central to understanding ecosystem response. This research will allow turfgrass managers to make more informed decisions about their management practices, and will also be relevant to sustainable management decisions using compost treatments on diverse agricultural crops.<br>
* ''SWES-MEL scientists involved: Vytas Pabedinskas, Bree Gomez''<br>
* ''SWES-MEL scientists involved: Vytas Pabedinskas, Bree Gomez''<br>
Line 29: Line 29:
''
''
-
<font color=blue>'''The “Central Dogma” Project, aka Deconstructing scaling ’from genes to ecosystems’: quantifying the relationship of molecular indices andcarbon fluxes in isolates and thawing permafrost
+
<font color=blue><big><big>'''The “Central Dogma” Project, aka'''<br>
-
'''<br><font color=black>
+
'''Deconstructing scaling ’from genes to ecosystems’: quantifying the relationship of molecular indices andcarbon fluxes in isolates and thawing permafrost
 +
'''</big></big><br><font color=black>
To predict ecosystem and planetary response to a changing climate, scaling from microorganisms to ecosystem processes is required. We propose to meet this challenge of scaling from the genomic diversity of communities to ecosystem-scale processes, i.e. “from genes to ecosystems,” by deconstructing and quantifying the stepwise linkages involved. Specifically, we will move beyond metabolic potential (genomes and metagenomes) to measuring expressed metabolism (meta- transcriptomes and -proteomes) and quantitatively relating it to biogeochemical fluxes. We will do so for the greenhouse gas methane, in controlled laboratory incubations of key methane-cycling cultivars as well as natural communities (specifically, those of the thawing permafrost at our field site).<br>
To predict ecosystem and planetary response to a changing climate, scaling from microorganisms to ecosystem processes is required. We propose to meet this challenge of scaling from the genomic diversity of communities to ecosystem-scale processes, i.e. “from genes to ecosystems,” by deconstructing and quantifying the stepwise linkages involved. Specifically, we will move beyond metabolic potential (genomes and metagenomes) to measuring expressed metabolism (meta- transcriptomes and -proteomes) and quantitatively relating it to biogeochemical fluxes. We will do so for the greenhouse gas methane, in controlled laboratory incubations of key methane-cycling cultivars as well as natural communities (specifically, those of the thawing permafrost at our field site).<br>
* ''SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones'' <br>
* ''SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones'' <br>
* ''Collaborating Labs: Hinsby Cadillo-Quiroz (Arizona State University), Jeff Chanton (Florida State U), Scott Saleska (UA) ''
* ''Collaborating Labs: Hinsby Cadillo-Quiroz (Arizona State University), Jeff Chanton (Florida State U), Scott Saleska (UA) ''

Revision as of 00:18, 17 April 2014


Carbon cycling in thawing permafrost ecosystems
Permafrost stores ~a third of the world’s soil organic carbon, in a relatively inaccessible frozen form. Under continued climate warming, permafrost is projected to decrease 50% by 2050 and be virtually eliminated by century’s end. Thawed permafrost frequently becomes wetland, which is a major source of the potent greenhouse gas methane, thereby raising the potential for dramatic positive feedbacks to warming. Our interdisciplinary DOE-funded project (renewed in 2013) examines the effects of natural in situ permafrost thaw on carbon cycling, by examining an existing permafrost thaw gradient in subarctic Sweden. We are focusing high-resolution, cutting-edge microbial and biogeochemical investigations across the three habitats defining this gradient: intact permafrost, intermediate-thaw peat bog, and fully-thawed fen wetland. Our results are being integrated into a wetland ecosystem process model that predicts greenhouse gas emissions, and the lessons generalized for inclusion in global climate models (which do not include or poorly characterize permafrost thaw). SWES-MEL co-leads this work and is one of two microbial ecology labs on the project, and our focus is on molecular analyses of microbial community composition and activity (16S rRNA gene surveys, metagenomics, and metaproteomics). Through this work, we hope to address how permafrost thaw effects carbon cycling, predict the likelihood and magnitude of global warming feedbacks, and add a mechanistic framework for scaling from “genes to ecosystems” in this biome.

  • SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones, Gary Trubl, Moira Hough, Darya Anderson, Akos Owusu-Dommey, Morgan Binder, Maya Sederholm, Krystalle Diaz
  • Collaborating Labs: Gene Tyson (Australian Center for Ecogenomics), Scott Saleska (UA), Matt Sullivan (UA), Patrick Crill (Stockholm U, Sweden), Jeff Chanton (Florida State U), Nathan Verberkmoes (New England BioLabs), Ruth Varner, Changsheng Li and Steve Frolking (U New Hampshire), Elena Shevliakova (Princeton).

Microbiology in the Critical Zone: geomicrobiology, "hot spots and hot moments", and ecosystem services in the JRB-SCM CZO
Together with the University of Arizona lab of Dr. Rachel Gallery, our lab has recently begun microbial investigations within the Jemez River Basin – Santa Catalina Mountains Critical Zone Observatory (JRB-SCM CZO). This CZO, led by Jon Chorover, has developed a conceptual framework of (a) “hot spots and hot moments”, where landscape change occurs non-uniformly over space and time, for example occurring rapidly after major fire events (which our CZO just experienced in summer 2013), and (b) an energy/carbon flow equation ("EEMT", effective energy and mass transfer, developed by CZO PI Craig Rasmussen) that quantitatively describes critical zone landscape evolution. With the CZO renewal in summer 2013 (and a new inclusion of CZ ecosystem services in the research mission), our lab and the Gallery Lab have begun to bridge microbiology and CZO biogeochemistry in the context of water and soil processes, including decomposition, weathering, carbon stabilization, and carbon flow, and water purification. Our approach spans both physiological (Gallery Lab) and meta-omic (our lab) approaches.

  • SWES-MEL scientist involved: Robert Jones, Gayle Frost
  • Collaborating Labs: Rachel Gallery (UA), Jon Chorover (UA), and the broader JRB-SCM CZO Team (UA)

The Great Barrier Reef "Microbial Buffering" Project
One of the threats to global reef systems in general, including the Great Barrier Reef, is coastal pollution. In northeastern Australia extensive land-use change to agriculture over the last century has brought coastal pollution from herbicides, pesticides, nutrients, and organic matter. Our collaborator Gene Tyson put forth the hypothesis that coastal microbial and viral communities may "buffer" reefs from the full impacts of pollution by taking up and/or transforming contaminants, and he, Matt Sullivan and myself developed a project to test this hypothesis. We partnered with David Bourne and Britta Schaffelke of the Australian Institute of Marine Science, who run extensive existing monitoring programs of coastal water quality and reef health, so that we could layer microbial and viral investigations on top of this rich and highly relevant metadata.

  • SWES-MEL scientist involved: Lynn Massey
  • Collaborating Labs: Gene Tyson (Australian Center for Ecogenomics), Matt Sullivan (UA), David Bourne & Britta Schaffelke (Australian Institute of Marine Science)

Understanding the system response of soil to compost additions, in partnership with the UA Land Stewardship Program
Turf grass covers more land area in the US than any agricultural crop, and has a higher chemical input than any agricultural crop. Managing it sustainably is key to minimizing its long-term impacts on water supply and watershed and atmosphere quality. The UA Land Stewardship Program has converted the management of the UA Mall’s turf grass from conventional to organic practices, after trials demonstrated that treating UA turfgrass with compost tea resulted in a range of system improvements, including decreased water use, increased C sequestration, deeper root depth, and the almost complete replacement of root-feeding nematodes by beneficial species (Pew and Hollar, 2011). Remarkably, compost tea application has also been shown to directly stimulate some plant “immune system” response, with increased protection from soil microbial and fungal pathogens; this response may be due to the direct physical interaction of compost-delivered microbes and plant root border cells (Curlango-Rivera, submitted). Reduction in fertilization should also reduce turf grass emissions of the greenhouse gas N2O, since its fluxes are strongly coupled to excess nitrogen related to fertilizer additions (Townsend-Small and Czimczik, 2010), however the full picture of compost effects on greenhouse gas emissions has not been performed. SWES-MEL is co-leading a team of UA researchers in a wholistic assessment of how compost treatments impact the soil community ecosystem and in turn influence greenhouse gas balance. Soil microorganisms are responsible for most below-ground carbon and nitrogen cycling, and therefore greenhouse has cycling, and so our lab’s research on the microbial communities is central to understanding ecosystem response. This research will allow turfgrass managers to make more informed decisions about their management practices, and will also be relevant to sustainable management decisions using compost treatments on diverse agricultural crops.

  • SWES-MEL scientists involved: Vytas Pabedinskas, Bree Gomez
  • Collaborators: van Haren Lab (Biosphere 2, UA), Chester Phillips (Compost Cats, UA), Troy Hollar (Merlin Organics), Gallery Lab (SNRE, UA), Hawes Lab (SWES, UA), Pavao-Zuckerman Lab (Biosphere 2, UA), Dontsova Lab (Biosphere 2, UA).

The “Central Dogma” Project, aka
Deconstructing scaling ’from genes to ecosystems’: quantifying the relationship of molecular indices andcarbon fluxes in isolates and thawing permafrost

To predict ecosystem and planetary response to a changing climate, scaling from microorganisms to ecosystem processes is required. We propose to meet this challenge of scaling from the genomic diversity of communities to ecosystem-scale processes, i.e. “from genes to ecosystems,” by deconstructing and quantifying the stepwise linkages involved. Specifically, we will move beyond metabolic potential (genomes and metagenomes) to measuring expressed metabolism (meta- transcriptomes and -proteomes) and quantitatively relating it to biogeochemical fluxes. We will do so for the greenhouse gas methane, in controlled laboratory incubations of key methane-cycling cultivars as well as natural communities (specifically, those of the thawing permafrost at our field site).

  • SWES-MEL scientists involved: Eun-Hae Kim, Robert Jones
  • Collaborating Labs: Hinsby Cadillo-Quiroz (Arizona State University), Jeff Chanton (Florida State U), Scott Saleska (UA)

Personal tools