Source: INDIANA UNIVERSITY submitted to
MICROBIAL SEED BANKS: PATTERNS AND MECHANISMS OF BACTERIAL DORMANCY IN SOILS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0233508
Grant No.
2011-67019-20661
Project No.
INDW-2013-02775
Proposal No.
2013-02775
Multistate No.
(N/A)
Program Code
A1401
Project Start Date
Feb 15, 2013
Project End Date
May 14, 2016
Grant Year
2013
Project Director
Lennon, J. T.
Recipient Organization
INDIANA UNIVERSITY
JORDAN HALL 142
BLOOMINGTON,IN 47401
Performing Department
Deparment of Biology
Non Technical Summary
Soils represent the largest reservoir of microbial diversity on Earth. Although we depend on soil microbes for a variety of critical ecosystem services, very little is known about the mechanisms that govern their abundance, diversity, and metabolic activity. Soils are subjected to a suite of natural and anthropogenic stressors, which in turn can have important implications for the structure and function of microbial communities. Some microorganisms can contend with such stressors by entering reversible state reduced state of metabolic activity, or dormancy. In this proposal, we outline a research plan that will use a combination of genomic and metagenomic to quantify the prevalence and dynamics of microbial dormancy in agricultural fields with different land use histories and precipitation regimes. The results will improve our understanding between the structure and function of microbes in soil ecosystems, while providing insight into the general features that allow for the persistence of microbes in nature, which is important for understanding pests and disease.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
10201101100100%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships;

Subject Of Investigation
0110 - Soil;

Field Of Science
1100 - Bacteriology;
Goals / Objectives
The objectives of the project are to 1) Identify the genetic mechanisms that allow soil bacteria to enter and exit dormancy in response to environmental stress (i.e., desiccation) using comparative genomics of reference strains isolated from soils. 2) Measure the expression of known and potentially novel dormancy genes in soils from different land-use histories exposed to altered precipitation regimes using stable isotope probing (SIP) and metagenomics. 3) Test theory about the contribution of dormant taxa to the dynamics and activity of soil microbial communities using manipulative field experiments.
Project Methods
1) To better understand the phylogenetic distribution of dormancy potential, we will sequence the genomes of bacteria isolated with novel enrichment techniques. We will then use comparative genomics to map the distribution of dormancy potential. 2) We propose to metagenomic approaches, possibly in combination of heavy-water stable isotope probing (SIP), to make inferences about genes that are expressed during the transition out of dormancy upon soil rewetting. 3) We will conduct a field experiment that manipulates precipitation, along with RNA and DNA based characterization of microbial communities, to assess the dynamics of dormancy in an agricultural landscape.

Progress 02/15/13 to 05/14/16

Outputs
Target Audience: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 processes. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided opportunities for two postdoctoral researchers. Dr. Sarah Placella worked on the field experiments that manipulated rainfall. Placella moved on to another postdoctoral position at Institut National de la Recherche Agronomique, Montpellier, France. She is now employed as a consultant at Servident, Inc. In late 2013, I hired a computational biologist, Dr. Ken Locey as a postdoctoral research to assist with data analysis related to the dormancy of microbial communities. Ms. Kayla Miller was a student in my lab who is conducted research to understand how dormancy affects the biogeographic distributions of bacteria in agricultural and forested landscapes. She is now pursuing her Ph.D. in microbial ecology. Mr. Mario Muscarella has helped with genome assembly and annotation. How have the results been disseminated to communities of interest?In addition to publishing papers in peer-reviewed publications, our group has presented related research at a variety of seminars, round tables, and conferences: " Guest presentation/instructor: EDAMAME course: Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology, Michigan State University " Introductory speaker and Guest Instructor: Summer Soil Institute at Colorado State University " Special Session: Rewetting Dry Soil: The Centurys Unifying Problem in Soil Microbial Ecology. ESA, Baltimore, MD " Special Session entitled "Seeing the trees for the forest: deciphering the biodiversity of soils ISME, Seoul, Korea " Rouge roundtable panelist Sleeping beauties: dormancy of bacteria in nature ISME, Seoul, Korea " Special symposium: Communities writ small: Integrating microbial systems into community ecology. ESA, Sacramento, CA " Guest presentation/instructor: EDAMAME course: Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology, Michigan State University " Keynote speaker, 5th Annual Argonne Soil Metagenomics Meeting, Bloomingdale, IL " Keynote speaker, XIII Symposium on Aquatic Microbial Ecology, Stresa, Italy " Special session: Impact of bacteriophage in the environment. Society for General Microbiology (SGM) Sussex University, East Sussex, UK " Special session: Ecological theory in microbial ecology, ESA, Minneapolis, MN " Special symposium: Integrating soil biodiversity into discussions of global sustainability: the time is now. ESA, Minneapolis, MN " Special symposium: The plant microbiome, Canadian Society for Ecology and Evolution, Kelowna, British Columbia, Canada (declined) " Keynote speaker, Understanding, managing and protecting microbial communities in aquatic and terrestrial ecosystems: Exploring the trait-based functional biodiversity approach. ESF Eurocores Ecological and Evolutionary Functional Genomics (EuroEEFG) workshop. Wageningen, The Netherlands " Special session on Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems. ASLO, New Orleans, LA " Aarhus University, Denmark, Microbial life under extreme energy limitation " Introductory talk for special session on Global browning of inland waters: implications of changing terrestrial dissolved organic carbon concentrations for aquatic ecosystems. ESA, Portland, OR " Duke University, University Program in Ecology " East Carolina University, Department of Biology " Hobart and William Smith Colleges (web-based seminar) " Center for the Integrative Study of Animal Behavior (CISAB), Indiana University " Vietnam National University, Department of Microbiology " University of Tennessee, Department of Ecology & Evolutionary Biology " University of Louisville, Department of Biology " University of Illinois, Program in Ecology, Evolution and Conservation Biology " Indiana University East and Earlham College, School of Natural Science and Mathematics " University of Kentucky, Department of Plant & Soil Sciences " Loyola University Chicago, Department of Biology " Miami University, Ecology, Evolution, and Environmental Biology " Purdue University, Department of Biological Sciences, Ecology and Evolutionary Biology " University of Texas at Austin, Section of Integrative Biology " University of Oregon, Institute of Ecology and Evolutionary Biology " University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology " The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands " University of Michigan, Department of Ecology and Evolutionary Biology " Virginia Tech, Department of Biological Sciences " Northwestern University, Biological Sciences " University of Jyv�skyl�, Finland, Department of Biological and Environmental Science " University of Quebec at Montreal, Canada, Department of Biological Sciences " Special session co-organizer. Trait-based ecology at the microscale. Ecological Society of America. Baltimore, MD " Special session co-organizer: Microbially mediated ecosystem services: The good, the bad and the ugly. Joint Aquatic Sciences Meeting. Portland, OR " Organizing committee: First Israel-U.S. Kavli Frontiers of Science symposium, Israel Academy of Sciences, U.S. National Academy of Sciences, and the Kavli Foundation What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Activity 1: We have extracted DNA from ~20 isogenic soil bacteria isolates and had them sequenced using Ilumina GAII technology at the MSU core sequencing facility. We have created in-lab databases and computing infrastructure to that has allowed us to assemble and annotate these genomes. We are using these data to conduct comparative genomic analyses to identify functional traits that correspond with physiologically based characterizations of the microbial niche. In addition, we have developed a laboratory assay to measure survivorship during dormancy to desiccation stress, which has provided us with a mean of characterizing the dormancy potential of diverse microbial taxa. Activity 2: Based on analysis of existing shotgun metagenomic libraries, we have been building a reference database containing genes that encode for resuscitation promoting factors (Rpf). These data have come from more than 1400 bacterial reference genomes. Rpf is a protein that has been shown in the literature to terminate dormancy in Gram-positive bacteria. We have amplified, cloned, and expressed recombinant Rpf and are using this to manipulate that dormant seed banks of various soil samples to test hypotheses regarding the Great Plate Anomaly.

Publications

  • Type: Journal Articles Status: Under Review Year Published: 2015 Citation: Peralta AL, Sun Y, Lennon JT (In Review) Crop diversity enhances disease suppressive potential in soils. bioRxiv Preprint doi:http://dx.doi.org/10.1101/030528
  • Type: Journal Articles Status: Under Review Year Published: 2015 Citation: Locey KJ, Lennon JT (2015) Scaling laws predict global microbial diversity. PeerJ PrePrints 3:e1808 doi:https://dx.doi.org/10.7287/peerj.preprints.1451v1
  • Type: Journal Articles Status: Under Review Year Published: 2015 Citation: Shoemaker WR, Locey KJ, Lennon JT (2015) Do modern theories of biodiversity fail to predict commonness and rarity among microbes? PeerJ PrePrints 3:e1806 doi:https://dx.doi.org/10.7287/peerj.preprints.1450v1
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Shoemaker WR, Muscarella ME, Lennon JT (2015) Genome sequence of the soil bacterium Janthinobacterium sp. KBS0711. Genome Announcements 3: e00689-15 (pdf)
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Lennon JT, Denef VJ (2015) Evolutionary ecology of microorganisms: from the tamed to the wild, p 4.1.2-1�4.1.2-12. In Yates MV, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, 4th ed. ASM Press, Washington, DC. [Epub ahead of print] doi:10.1128/9781555818821.ch4.1.2. PeerJ Preprint. doi:https://dx.doi.org/10.7287/peerj.preprints.1025v1
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Aanderud ZT, Jones SE, Fierer N, Lennon JT (2015) Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Frontiers in Microbiology 6:24
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Peralta AL, Stuart D, Kent AD, Lennon JT (2014) A social-ecological framework for "micromanaging" microbial services. Frontiers in Ecology and the Environment 12: 524-531
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lennon JT, SE Jones (2015) Ecological and evolutionary insight into the persistence of soil bacteria. Argonne Soils Workshop, Argonne National Laboratory, Argonne, IL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Peralta, AP, Sun Y, Lennon JT (2015) Effects of crop diversity on plant-soil-microbial interactions. LTER All Scientist Meeting, Estes Park, CO
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lau JA, Lennon JT, terHorst CP (2015) The interplay of ecology and evolution in aboveground-belowground response to environmental change. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Aanderud ZT, Jones SE, Fierer N, Lennon JT (2015) Resuscitation of the rare biosphere contributes to pules of ecosystem activity following soil rewetting. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: terHorst CP, Lennon JT, Lau JA (2015) Plant evolution in response to drought alters the structure and function of soil microbial communities. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lennon JT, Jones SE (2015) A trait-based approach to microbial dormancy. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Locey KJ, Lennon JT (2015) Residence time: An overlooked constraint on community assembly and structure. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Treseder KK, Lennon JT (2015) Fungal traits that drive ecosystem dynamics. Ecological Society of America, Baltimore, MD
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lennon JT, Jones SE (2015) Bacterial persistence during starvation: dormancy, cannibalism, and adaptation. American Society of Microbiology, New Orleans, LA


Progress 02/15/14 to 02/14/15

Outputs
Target Audience: 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 processes. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project has provided opportunities for two postdoctoral researchers. Dr. Sarah Placella worked on the field experiments that manipulated rainfall. Placella has now moved on to another postdoctoral position at Institut National de la Recherche Agronomique, Montpellier, France. In late 2013, I hired a computational biologist, Dr. Ken Locey as a postdoctoral research to assist with data analysis related to the dormancy of microbial communities. Ms. Kayla Miller is Ph.D. student in my lab who is conducting research to understand how dormancy affects the biogeographic distributions of bacteria in agricultural and forested landscapes. Mr. Mario Muscarella has helped with genome assembly and annotation. How have the results been disseminated to communities of interest? In addition to publishing papers in peer-reviewed publications, our group has presented related research at a variety of seminars, roundtables, and conferences: Invited Seminar: University of Tennessee, Department of Ecology & Evolutionary Biology Invited Seminar: University of Illinois, Program in Ecology, Evolution and Conservation Biology Invited Seminar: Miami University, Ecology, Evolution, and Environmental Biology Guest instructor: “EDAMAME course: Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology”, Michigan State University Invited seminar: Indiana University East and Earlham College, School of Natural Science and Mathematics Invited seminar: University of Kentucky, Department of Plant & Soil Sciences Invited speaker: Special Session entitled "Seeing the trees for the forest: deciphering the biodiversity of soils” ISME, Seoul, Korea Invited speaker: Loyola University Chicago, Department of Biology Invited Speaker: Special symposium: “Communities writ small: Integrating microbial systems into community ecology”. ESA, Sacramento, CA Invited Speaker: Purdue University, Department of Biological Sciences, Ecology and Evolutionary Biology terHorst CP, Lau JA, Lennon JT (2013) The relative importance of rapid evolution in plant-soil feedbacks depends on ecological context. Ecological Society of America, Minneapolis, MN Peralta AL, Lennon JT (2013) Legacy effects on soil microbial communities in human-dominated ecosystems. Ecological Society of America, Minneapolis, MN Organizing Committee: First Israel-U.S. Kavli Frontiers of Science symposium, Israel Academy of Sciences, U.S. National Academy of Sciences, and the Kavli Foundation Special symposium organizer: "Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them". ESA, Minneapolis, MN Co-investigator: John Wesley Powell Center for Analysis and Synthesis, "Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them". Fort Collins, CO Invited Speaker: University of Texas at Austin, Section of Integrative Biology Invited Keynote speaker, 5th Annual Argonne Soil Metagenomics Meeting, Bloomingdale, IL Invited Speaker: Special session: "Ecological theory in microbial ecology", ESA, Minneapolis, MN Invited Speaker: Special symposium: "Integrating soil biodiversity into discussions of global sustainability: the time is now". ESA, Minneapolis, MN Invited Speaker: University of Oregon, Institute of Ecology and Evolutionary Biology Invited Speaker: University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology Invited Keynote Speaker: The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands "Understanding, managing and protecting microbial communities in aquatic and terrestrial ecosystems:"Exploring the trait-based functional biodiversity approach". ESF Eurocores Ecological and Evolutionary Functional Genomics (EuroEEFG) workshop. Wageningen, The Netherlands Special session on "Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems". ASLO, New Orleans, LA Invited Speaker: University of Michigan, Department of Ecology and Evolutionary Biology What do you plan to do during the next reporting period to accomplish the goals? We will continue to analyze existing data; write manuscripts for publication in peer-review journals; communicate our research at scientific meetings; finish experiments related to the objectives of the proposed research.

Impacts
What was accomplished under these goals? Activity 1: We have extracted DNA from ~20 isogenic soil bacteria isolates and had them sequenced using Ilumina GAII technology at the MSU core sequencing facility. We have created in-lab databases and computing infrastructure to that has allowed us to assemble and annotate these genomes. We are using these data to conduct comparative genomic analyses to identify functional traits that correspond with physiologically based characterizations of the microbial niche. In addition, we have developed a laboratory assay to measure survivorship during dormancy to desiccation stress, which has provided us with a mean of characterizing the dormancy potential of diverse microbial taxa. Activity 2: Based on analysis of existing shotgun metagenomic libraries, we have been building a reference database containing genes that encode for resuscitation promoting factors (Rpf). These data have come from more than 1400 bacterial reference genomes. Rpf is a protein that has been shown in the literature to terminate dormancy in Gram-positive bacteria. We have amplified, cloned, and expressed recombinant Rpf and are using this to manipulate that dormant seed banks of various soil samples to test hypotheses regarding the Great Plate Anomaly.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: Peralta AL, Stuart D, Kent AD, Lennon JT. A social-ecological framework for "micromanaging" microbial services. Frontiers in Ecology and the Environment.
  • Type: Book Chapters Status: Under Review Year Published: 2014 Citation: Lennon JT, Denef VJ Evolutionary ecology of microorganisms: from the tamed to the wild. American Society of Microbiology. Manual of Environmental Microbiology.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Krause S, Le Roux X, Niklaus PA, Van Bodegom P, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier P (2014) Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Frontiers in Microbiology 5: 251
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: terHorst CP, Lennon JT, Lau JA (2014) The relative importance of rapid evolution for plant-soil feedbacks depend on ecological context. Proceeding of the Royal Society B. 281: 20140028


Progress 02/15/14 to 05/14/14

Outputs
Target Audience: 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 processes. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project has provided opportunities for two postdoctoral researchers. Dr. Sarah Placella worked on the field experiments that manipulated rainfall. Placella has now moved on to another postdoctoral position at Institut National de la Recherche Agronomique, Montpellier, France. In late 2013, I hired a computational biologist, Dr. Ken Locey as a postdoctoral research to assist with data analysis related to the dormancy of microbial communities. Ms. Kayla Miller is Ph.D. student in my lab who is conducting research to understand how dormancy affects the biogeographic distributions of bacteria in agricultural and forested landscapes. Mr. Mario Muscarella has helped with genome assembly and annotation. How have the results been disseminated to communities of interest? In addition to publishing papers in peer-reviewed publications, our group has presented related research at a variety of seminars, roundtables, and conferences: Invited Seminar: University of Tennessee, Department of Ecology & Evolutionary Biology Invited Seminar: University of Illinois, Program in Ecology, Evolution and Conservation Biology Invited Seminar: Miami University, Ecology, Evolution, and Environmental Biology Guest instructor: “EDAMAME course: Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology”, Michigan State University Invited seminar: Indiana University East and Earlham College, School of Natural Science and Mathematics Invited seminar: University of Kentucky, Department of Plant & Soil Sciences Invited speaker: Special Session entitled "Seeing the trees for the forest: deciphering the biodiversity of soils” ISME, Seoul, Korea Invited speaker: Loyola University Chicago, Department of Biology Invited Speaker: Special symposium: “Communities writ small: Integrating microbial systems into community ecology”. ESA, Sacramento, CA Invited Speaker: Purdue University, Department of Biological Sciences, Ecology and Evolutionary Biology terHorst CP, Lau JA, Lennon JT (2013) The relative importance of rapid evolution in plant-soil feedbacks depends on ecological context. Ecological Society of America, Minneapolis, MN Peralta AL, Lennon JT (2013) Legacy effects on soil microbial communities in human-dominated ecosystems. Ecological Society of America, Minneapolis, MN Organizing Committee: First Israel-U.S. Kavli Frontiers of Science symposium, Israel Academy of Sciences, U.S. National Academy of Sciences, and the Kavli Foundation Special symposium organizer: "Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them". ESA, Minneapolis, MN Co-investigator: John Wesley Powell Center for Analysis and Synthesis, "Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them". Fort Collins, CO Invited Speaker: University of Texas at Austin, Section of Integrative Biology Invited Keynote speaker, 5th Annual Argonne Soil Metagenomics Meeting, Bloomingdale, IL Invited Speaker: Special session: "Ecological theory in microbial ecology", ESA, Minneapolis, MN Invited Speaker: Special symposium: "Integrating soil biodiversity into discussions of global sustainability: the time is now". ESA, Minneapolis, MN Invited Speaker: University of Oregon, Institute of Ecology and Evolutionary Biology Invited Speaker: University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology Invited Keynote Speaker: The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands "Understanding, managing and protecting microbial communities in aquatic and terrestrial ecosystems:"Exploring the trait-based functional biodiversity approach". ESF Eurocores Ecological and Evolutionary Functional Genomics (EuroEEFG) workshop. Wageningen, The Netherlands Special session on "Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems". ASLO, New Orleans, LA Invited Speaker: University of Michigan, Department of Ecology and Evolutionary Biology What do you plan to do during the next reporting period to accomplish the goals? We will continue to analyze existing data; write manuscripts for publication in peer-review journals; communicate our research at scientific meetings; finish experiments related to the objectives of the proposed research.

Impacts
What was accomplished under these goals? Activity 1: We have extracted DNA from ~20 isogenic soil bacteria isolates and had them sequenced using Ilumina GAII technology at the MSU core sequencing facility. We have created in-lab databases and computing infrastructure to that has allowed us to assemble and annotate these genomes. We are using these data to conduct comparative genomic analyses to identify functional traits that correspond with physiologically based characterizations of the microbial niche. In addition, we have developed a laboratory assay to measure survivorship during dormancy to desiccation stress, which has provided us with a mean of characterizing the dormancy potential of diverse microbial taxa. Activity 2: Based on analysis of existing shotgun metagenomic libraries, we have been building a reference database containing genes that encode for resuscitation promoting factors (Rpf). These data have come from more than 1400 bacterial reference genomes. Rpf is a protein that has been shown in the literature to terminate dormancy in Gram-positive bacteria. We have amplified, cloned, and expressed recombinant Rpf and are using this to manipulate that dormant seed banks of various soil samples to test hypotheses regarding the Great Plate Anomaly.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: Peralta AL, Stuart D, Kent AD, Lennon JT. A social-ecological framework for "micromanaging" microbial services. Frontiers in Ecology and the Environment.
  • Type: Book Chapters Status: Under Review Year Published: 2014 Citation: Lennon JT, Denef VJ Evolutionary ecology of microorganisms: from the tamed to the wild. American Society of Microbiology. Manual of Environmental Microbiology.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Krause S, Le Roux X, Niklaus PA, Van Bodegom P, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier P (2014) Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Frontiers in Microbiology 5: 251
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: terHorst CP, Lennon JT, Lau JA (2014) The relative importance of rapid evolution for plant-soil feedbacks depend on ecological context. Proceeding of the Royal Society B. 281: 20140028


Progress 02/15/13 to 02/14/14

Outputs
Target Audience: 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 processes. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project has provided opportunities for two postdoctoral researchers. Dr. Sarah Placella worked on the field experiments that manipulated rainfall. Placella has now moved on to another postdoctoral position at Institut National de la Recherche Agronomique, Montpellier, France. In late 2013, I hired a computational biologist, Dr. Ken Locey as a postdoctoral research to assist with data analysis related to the dormancy of microbial communities. Ms. Kayla Miller is Ph.D. student in my lab who is conducting research to understand how dormancy affects the biogeographic distributions of bacteria in agricultural and forested landscapes. How have the results been disseminated to communities of interest? In addition to publishing papers in peer-reviewed publications, our group has presented related research at a variety of seminars, roundtables, and conferences: terHorst CP, Lau JA, Lennon JT (2013) The relative importance of rapid evolution in plant-soil feedbacks depends on ecological context. Ecological Society of America, Minneapolis, MN Peralta AL, Lennon JT (2013) Legacy effects on soil microbial communities in human-dominated ecosystems. Ecological Society of America, Minneapolis, MN Organizing Committee: First Israel-U.S. Kavli Frontiers of Science symposium, Israel Academy of Sciences, U.S. National Academy of Sciences, and the Kavli Foundation Special symposium organizer: “Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them”. ESA, Minneapolis, MN Co-investigator: John Wesley Powell Center for Analysis and Synthesis, “Next generation of ecological indicators: defining which microbial properties matter most to ecosystem function and how to measure them”. Fort Collins, CO University of Texas at Austin, Section of Integrative Biology Keynote speaker, 5th Annual Argonne Soil Metagenomics Meeting, Bloomingdale, IL Special session: “Ecological theory in microbial ecology”, ESA, Minneapolis, MN Special symposium: “Integrating soil biodiversity into discussions of global sustainability: the time is now”. ESA, Minneapolis, MN University of Oregon, Institute of Ecology and Evolutionary Biology University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology Special symposium: “The plant microbiome”, Canadian Society for Ecology and Evolution, Kelowna, British Columbia, Canada (declined) The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands Keynote speaker, “Understanding, managing and protecting microbial communities in aquatic and terrestrial ecosystems: “Exploring the trait-based functional biodiversity approach”. ESF Eurocores Ecological and Evolutionary Functional Genomics (EuroEEFG) workshop. Wageningen, The Netherlands Special session on “Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems”. ASLO, New Orleans, LA University of Michigan, Department of Ecology and Evolutionary Biology What do you plan to do during the next reporting period to accomplish the goals? We will continue to analyze existing data; write manuscripts for publication in peer-review journals; communicate our research at scientific meetings; finish experiments related to the objectives of the proposed research.

Impacts
What was accomplished under these goals? Activity 1: We have extracted DNA from ~20 isogenic soil bacteria isolates and had them sequenced using Ilumina GAII technology at the MSU core sequencing facility. The sequences have been assembled and annotated. We have used these data to conduct comparative genomic analyses to identify functional traits that correspond with physiologically based characterizations of the microbial niche. In addition, we have developed a laboratory assay to measure survivorship during dormancy to desiccation stress, which has provided us with a mean of characterizing the dormancy potential of diverse microbial taxa. Activity 2: Based on analysis of existing shotgun metagenomic libraries, we have been building a reference database containing genes that encode for resuscitation promoting factors (Rpf). These data have come from more than 1400 bacterial reference genomes. Rpf is a protein that has been shown in the literature to terminate dormancy in Gram-positive bacteria. We have amplified, cloned, and expressed recombinant Rpf and are using this to manipulate that dormant seed banks of various soil samples to test hypotheses regarding the Great Plate Anomaly. Activity 3: In the summer of 2011, we constructed rainout shelters to conduct precipitation manipulations in two land use types on the KBS LTER (row crop agriculture and successional grassland). We were able to successfully reduced rainfall by 75% relative to ambient shelters where rainfall was collected and reapplied. This had strong effects on soil water potential. We measured gas flux from the sites using sensor technology and more traditional measures. We sequenced the 16S rRNA genes (rDNA) and transcripts (rRNA) from key times in this experiment. We found major discrepancies between the diversity and composition of microorganisms when characterized by RNA vs. DNA. Furthermore, we found that the RNA:DNA ratio of taxa is strongly drive by water potential.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lauber CL, Ramirez KS, Aanderud ZT, Lennon JT, Fierer N. (2013) Temporal variability in soil microbial communities across land-use types. The ISME Journal 7: 1641-1650
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Aanderud ZT, Jones SE, Schoolmaster DR, Fierer N, Lennon JT (2013) Sensitivity of soil respiration and microbial communities to altered snowfall. Soil Biology & Biochemistry 57: 217227