Source: UNIVERSITY OF FLORIDA submitted to NRP
INTERACTIONS OF SYMBIOTIC BACTERIA AND THEIR ENVIRONMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1000268
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Jan 10, 2014
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Microbiology and Cell Science
Non Technical Summary
The overall objective of this research is to examine the interactions between microbes and their surrounding environment to improve our understanding of the molecular mechanisms that microbes use to adapt and respond to changes in the environment. To address this overarching goal I propose to use two model systems to examine how microbes form symbiotic interactions and how they are impacted by their environment. These two systems include: 1) modern microbialites (i.e., lithifying microbial biofilms), where hundreds of bacterial species form symbiotic associations that ultimately lead to the sequestration of carbon as calcium carbonate; and 2) a simplified symbiosis between a luminescent bacterium Vibrio fischeri and its animal host Euprymna scolopes, which leads to extensive bacteria-induced development in the host tissues. These two model systems provide two distinct approaches to assess how microbes interact with other living cells and their surrounding environment.
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
3063999104050%
1354010104050%
Knowledge Area
135 - Aquatic and Terrestrial Wildlife; 306 - Environmental Stress in Animals;

Subject Of Investigation
3999 - Animal research, general; 4010 - Bacteria;

Field Of Science
1040 - Molecular biology;
Goals / Objectives
The overall objective of this research is to examine the interactions between microbes and their surrounding environment to improve our understanding of the molecular mechanisms that microbes use to adapt and respond to changes in the environment. To address this overarching goal I propose to use two model systems to examine how microbes form symbiotic interactions and how they are impacted by their environment. These two systems include: 1) modern microbialites (i.e., lithifying microbial biofilms), where hundreds of bacterial species form symbiotic associations that ultimately lead to the sequestration of carbon as calcium carbonate; and 2) a simplified symbiosis between a luminescent bacterium Vibrio fischeri and its animal host Euprymna scolopes, which leads to extensive bacteria-induced development in the host tissues. These two model systems provide two distinct approaches to assess how microbes interact with other living cells and their surrounding environment. Specifically, using Model System 1 my objectives will be to: Objective 1. Assess how complex microbialites are spatially organized and delineate themetabolic potential of these lithifying microbial communities to modify their environment and promote carbonate mineralization. Objective 2. Determine the functional complexity of microbialite transcriptome andcharacterize how the transcriptome is spatially and temporally regulated within the microbialite. Additionally, using Model System 2 my objectives will be to: Objective 3. Characterize changes in the V. fischeri symbiont and E. scolopes hosttranscriptome in response to microgravity, a form of environmental stress. Objective 4. Examine the changes in the V. fischeri-induced immune response of hostanimal tissues under a simulated microgravity environment.
Project Methods
Methodology Objective 1. Assess how complex microbialites are spatially organized and delineate the metabolic potential of these lithifying microbial communities to modify their environment and promote carbonate mineralization. Approach: Barcoded-SSU rRNA genes and multiplex high-throughput DNA sequencing. To directly compare the microbial diversity within different depths of the microbialites we propose to use high throughput barcoded 16S and 18S rRNA gene analyses using an Illumina MiSeq sequencing platform now available at the University of Florida sequencing core facility. Objective 2. Determine the functional complexity of microbialite transcriptome and characterize how the transcriptome is spatially and temporally regulated within the microbialite. Approach: High throughput sequencing the microbialitic mat metatranscriptome. To complement the microbial diversity results the gene expression patterns in the mats will be examined first in using the same samples as Objective 1, generating a highly detailed and integrated data set. cDNA libraries (1μg) for each sample will be created and sequenced using the Illumina HiSeq 2000 platform at the UF facilities. Objective 3. Characterize changes in the V. fischeri symbiont and E. scolopes host transcriptome in response to microgravity, a form of environmental stress. Approach 1. Simulating Microgravity Conditions - To complete this research we will simulate microgravity conditions using high-aspect-ratio rotating wall vessel bioreactors (HARVs) developed by the NASA Biotechnological Group (JSC, Houston, TX; Wolf and Schwarz, 1991; Schwarz et al., 1992). Approach 2. Transcriptome sequencing of host light organ exposed to microgravity. To examine the impact of microgravity on the host squid in the presence and absence of V. fischeri the transcriptome of the host squid will be partially sequenced using RNAseq, or direct transcriptome sequencing with the high throughput Illumina sequencing platform. Approach 3 - Expression of metabolically active genes under microgravity using quantitative real time PCR (qPCR). To independently confirm results derived from Approach 2 genes of interest will further characterized using qPCR. Objective 4. Examine the changes in the V. fischeri induced immune response of host animal tissue under a simulated microgravity environment. Approach 1: Effects of exogenous V. fischeri peptidoglycan and peptidoglycan derivatives on hemocyte trafficking under simulated microgravity conditions. Approach 2. Measure background levels of V. fischeri peptidoglycan in the surrounding medium under microgravity conditions. In addition to examining the effects of microgravity on exogenously added peptidoglycan to the host squid, we propose to determine whether simulated microgravity conditions alter the normal shedding of V. fischeri peptidoglycan into the surrounding medium. Approach 3: Examining mucus production in response to microgravity. Mucus production by the ciliated epithelial appendages (CEA) is a critical mechanism to facilitate the normal biofilm formation and colonization of the host light organ by V. fischeri. V. fischeri will not adhere to the surface of the CEA in the absence of mucus. Approach 4: Examine changes in NF-kB pathway using quantitative PCR. The nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) pathway is found in almost all animal cell types and is a key regulator of the host innate immune response (Silverman et al., 2001). The NF-kB pathway, which has been identified in E. scolopes (Goodson et al., 2005), is often activated by MAMPs including LPS and peptidoglycan (Janeway et al., 1989).

Progress 01/10/14 to 09/30/18

Outputs
Target Audience:There were two target audiences for the outputs of this Hatch project for this reporting period. The first audience was the astrobiology and environmental microbiology scientific communities. The second area was the space biology and host-microbe interactions scientific communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This work has provided the opportunity for the training of three underrepresented undergraduates, four graduate students, and one postdoctoral fellow. One graduate student, who used the work outlined in Objectives 1/2 completed her PhD in July 2017 and has two peer-reviewed manuscripts, with another in review. She is now a postdoctoral fellow at the University of Connecticut. Another graduate student, who has focused on Objective 2, was awarded a NASA NESSF fellowship for her work and is expected to graduate next year. Two additional students are using the research from Objectives 3/4 for their own dissertation research. All of the graduate students and post-doc have attended both regional and national-level meetings to present their work. How have the results been disseminated to communities of interest?In the past five years there has been a total of 22 peer reviewed publications, 16 presentations at both local, national and international meetings. I have also given 16 seminars at various universities and organizations across the globe. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The objectives of this project were as follows: 1) Assess how complex microbialites are spatially organized and delineate themetabolic potential of these lithifying microbial communities to modify their environment and promote carbonate mineralization; Determine the functional complexity of microbialite transcriptome andcharacterize how the transcriptome is spatially and temporally regulated within the microbialite; 3) Characterize changes in the V. fischeri symbiont and E. scolopes hosttranscriptome in response to microgravity, a form of environmental stress; and 4) Examine the changes in the V. fischeri-induced immune response of hostanimal tissues under a simulated microgravity environment. The outcomes of these scientific objectives were as follows: 1. We identified several new molecular pathways by which microbialites (i.e., deposits of calcium carbonate made my microbes) are formed under environmental stress conditions. 2. We determined how the genes within a microbialite change over the course of a day and year under natural environmental conditions. We also built a network of how the expression of the genes change to assess how microbial community changes under different environmental conditions. 3. We determined that under simulated microgravity conditions, having beneficial symbionts present can reduce the onset of an environmental stress in host animals. 4. We determined that the beneficial microbe V. fischeri was not significantly or negatively impacted by simulated microgravity conditions. These results suggest that beneficial microbes may not be significantly altered during actual space flight. Deliverables: 1. We sequenced the genome and transcriptome of the host squid Euprymna scolopes providing an important tool for the science community. All the sequencing data we generated has been made public.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Louyakis, Artemis S., Hadrien Gourlé, Giorgio Casaburi, Rachelle ME Bonjawo, Alexandrea A. Duscher, and Jamie S. Foster. "A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles." Environmental microbiology 20, no. 2 (2018): 842-861.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Babilonia, Joany, Jamie S. Foster, Ana Conesa, Giorgio Casaburi, Cecile Pereira, Artemis Louyakis, and Ruth Pamela Reid. "Comparative metagenomics provides insight into the ecosystem functioning of the Shark Bay stromatolites, Western Australia." Frontiers in microbiology 9 (2018): 1359.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Alexandrea A. Duscher, Ana Conesa, Mary Bishop, Madeline M. Vroom, Sergio D. Zubizarreta & Jamie S. Foster (2018)Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity. npj Microgravity 25(4)


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:There were two target audiences for the outputs of this Hatch project for this reporting period. The first audience was the astrobiology and environmental microbiology scientific communities. The second area was the space biology and host-microbe interactions scientific communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This work has provided the opportunity for the training of two underrepresented undergraduate, four graduate students, and one postdoctoral fellow. One graduate student, who used the work outlined in Objectives 1/2 completed her PhD in July 2017 and has two peer-reviewed manuscripts, with another in review. She is now a postdoctoral fellow at the University of Connecticut. Another graduate student, who has focused on Objective 2, was awarded a NASA NESSF fellowship for her work and is expected to graduate next year. Two additional students are using the research from Objectives 3/4 for their own dissertation research. All of the graduate students and post-doc have attended both regional and national-level meetings to present their work, including the 2017 Astrobiology Science Conference, 2017 Host-Microbe Interactions meeting and the 2017 Florida Branch of the American Society for Microbiology. How have the results been disseminated to communities of interest?A total of three peer-reviewed publications have been disseminated to the science community. I have presented this work at two national meetings and one international meeting. I have also given two public lectures on this work at other Florida Universities. What do you plan to do during the next reporting period to accomplish the goals?Objective 1 - Although the original tasks associated with this objective are complete, we expanded this objective to also include a metabolomics analysis of the Australian stromatolites. We plan to analyze those data and prepare amanuscript onthat work. Objective 2 - We have completed this task, but hope to do additional network analysis of the data and annotate the genomes of several of the dominant taxa within the Bahamian thrombolites. Objective 3 & 4 - As this work has been completed we plan to use the sequenced transcriptome as a foundation for additional analysis of the host animal immune system under simulated microgravity conditions. We also plan on preparing two manuscripts based on this additional research in 2018.

Impacts
What was accomplished under these goals? Objective 1 - Although the majority of this work was completed in 2015/2016, we completed an updated metagenomic and 16S rRNA gene analysis of the dominant metabolisms within two major types of microbialites: thrombolites (The Bahamas) and stromatolites (Shark Bay, Western Australia). We also isolated one of the dominant cyanobacteria from the Bahamian thrombolites and sequenced the genome. One manuscript was published in 2017 based on this work and two more manuscripts are in preparation Objective 2 - This project was completed in 2017 and we generated the first metatranscriptome of a modern microbialite. The work revealed distinctive diel and seasonal patterns of gene expression within the thrombolites that provided important insight into the formation of these ancient structures. A manuscript based on these results has been accepted for publication in 2017. Objective 3 - This work was primarily completed in 2016, but the manuscript based on this work was published in early 2017. Our key finding was that the symbiotic microbes of the host animal, Euprymna scolopes, helped modulate the innate immune response during modeled microgravity conditions. We hope to use the results of this work as a foundation for understanding how the immune system of animals are impacted by space flight. Objective 4 - In 2016 we sequenced and assembled the transcriptome of the model organism, Euprymna scolopes. We used this information to assemble the genome of the animal and are in the process of preparing this work for publication.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chaturvedi, P., DC Vanegas, BA Hauser, JS Foster, MS Sepulveda and EM McLamore* (2017) Microprofiling real-time nitric oxide flux for field studies using a stratified nanohybrid carbon-metal electrode. Analytical Methods 9, 6061
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Casaburi, G, I Goncharenko-Foster, AA Duscher and JS Foster (2017) Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions. Scientific Reports 7:46318
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Louyakis, AS, JM Mobberley, BE Vitek, PT Visscher, PD Hagan, RP Reid, R. Kozdon, IJ Orland, JW Valley, NJ Planavsky, G. Casaburi, JS Foster (2017) A study of the microbial spatial heterogeneity of Bahamian thrombolites using molecular, biochemical, and stable isotope analyses. Astrobiology 17(5): 413-430.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience: There were two target audiences for the outputs of this Hatch project for this reporting period. The first audience was the astrobiology and environmental microbiology scientific communities. The second area was the space biology and host- microbe interactions scientific communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This work has provided the opportunity for the training of undergraduate and graduate students as well as a postdoctoral fellow. For example, one undergraduate and two graduate students worked on objectives 1 and 2. Both of the graduate students, Dyanna Louyakis and Joany Babilonia are using this work as part of her PhD dissertation. In objectives 3 and 4, one undergraduate, one graduate student, and one postdoctoral fellow have worked on this project this. Graduate student Lexi Duscher is using this work as the basis of her PhD dissertation. Additionally, all of the graduate students and post-doc have attended both regional and national-level meetings to present their work, including the 2016 Host Microbe Interactions meeting in Honolulu, HI and the 2016 Florida Branch of the American Society for Microbiology. How have the results been disseminated to communities of interest?A total of six peer reviewed publications have been disseminated to the science community. I have presented this work at two national meetings and generated an educational video in conjunction with Bush Heritage Australia. The video s currently on my you tube channel and available to the public. What do you plan to do during the next reporting period to accomplish the goals?Objectives 1/3 - The work associated with Objectives 1 and 3 are essentially complete and we anticipate two additional manuscripts to be published based on this work. Objective 2 - we have completed the assembly of the 50 metagenomes and anticipate additional bioinformative analysis on these data sets to be completed in 2017. The metatranscriptomic paper is currently in preparation and we hope to have that submitted in Spring of 2017. Objective 4 - We now have completed the reference transcriptome of the host animal using a new PacBio IsoSeq technology and we are collaborating with the E. scolopes genome team to publish our work this spring.

Impacts
What was accomplished under these goals? Objective 1 - The research associated with this objective was completed in 2015 and in 2016 we published two manuscripts based on these findings. Our findings showed that the salinity of the environment was a major driver of microbial diversity in the hypersaline waters of Hamelin Pool, Shark Bay, Western Australia. Additionally, we found distinct taxonomic and metabolic stratifications in the thrombolites of the Bahamas, which further confirmed that these communities are distinctive microbialites. Objective 2 - We completed the sequencing of 50 metagenomes of modern stromatolites from across the globe and are in the process of assembling the metagenomes and characterizing the similarities between modern lithifying stromatolites from across the globe. We also completed the first metabolomic analysis of modern stromatolites for the Shark Bay stromatolites and are in the process of analyzing the data.Lastly, we completed the data analysis of the metatranscriptome of modern thrombolites and are in the process of preparing those results into a manuscript. Objective 3 - The analysis of the E. scolopes host transcriptome in response to microgravity has been complete and we submitted a manuscript about those findings that are in review. Our results suggest that the microbes might help regulate the immune system of the host animal during modeled microgravty. Additionally, we have completed the analysis of the V. fischeri (symbiont) transcriptome in response to modeled microgravity andare in the process of preparing the manuscript for publication. Objective 4 - We generated a reference transcriptome of the host organism and are in the process of using this information to assembly the genome of the host organism. we are then using the reference transcriptome to idenitfy differentially expressed genes associated with the immune system. We hope to have this published in 2017.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Casaburi, G, AA Duscher, RP Reid, and JS Foster* (2016) Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis. Environmental Microbiology 18: 1452-1469
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Suosaari, EP, RP Reid*, PE Playford, JS Foster, JF Stolz, G Casaburi, PD Hagan, V Chirayath, IG Macintyre, NJ Planavsky, and GP Eberli (2016) New Insight into Stromatolite Formation in Shark Bay, Western Australia. Scientific Reports 6, 20557; doi: 10.1038/srep20557
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Paul, V, D Wronkiewicz, MR Mormile, JS Foster (2016) Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storrs Lake, The Bahamas. Astrobiology 16: 282-300
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Heath-Heckman, EA, JS Foster, MA Apicella, WE Goldman, MJ McFall-Ngai* (2016) Environmental cues and symbiont MAMPs function in concert to drive the daily remodeling of the crypt-cell brush border of the Euprymna scolopes light organ. Cellular microbiology. doi: 10.1111/cmi.12602
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Warden, JG, G. Casaburi, CR Omelon, PC Bennett, DO Breeker, and JS Foster* (2016) Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using whole shotgun metagenomics. Frontiers in Microbiology 7:1064
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Foster, JS (2016). Microbialite. In AccessScience. McGraw-Hill Education. https://doi.org/10.1036/1097-8542.422110
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Louyakis, AS, JM Mobberley, BE Vitek, PT Visscher, PD Hagan, RP Reid, R. Kozdon, IJ Orland, JW Valley, NJ Planavsky, G. Casaburi, JS Foster* (2016) A study of the microbial spatial heterogeneity of Bahamian thrombolites using molecular, biochemical, and stable isotope analyses. Astrobiology in press


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:There were two target audiences for the outputs of this Hatch project for this reporting period. The first audience was the astrobiology and environmental microbiology scientific communities. The second area was the space biology and host-microbe interactions scientific communities. Changes/Problems:As two of the students have graduated I have added graduate student Joany Babilonia and Lexi Duscher on to the project. What opportunities for training and professional development has the project provided?This work has provided the opportunity for the training of undergraduate and graduate students as well as a postdoctoral fellow. For example, one undergraduate and two graduate students worked on objectives 1 and 2. Both of the graduate students, Dyanna Louyakis and Joany Babilonia are using this work as part of her PhD dissertation. In objectives 3 and 4, one undergraduate, one graduate student, and one postdoctoral fellow have worked on this project this. Graduate student Lexi Duscher is using this work as the basis of her PhD dissertation. Additionally, all of the graduate students and post-doc have attended both regional and national-level meetings to present their work, including the 2015 Astrobiology Science Conference and Florida Branch of the American Society for Microbiology. How have the results been disseminated to communities of interest?The results have been presented as public lectures, scientific seminars, publications, and through laboratory tours. What do you plan to do during the next reporting period to accomplish the goals?Objective 1 - We plan to submit a manuscript on these results in spring of 2016. We also plan to expand the study sites to include additional types of microbialites and also collect samples for metatranscriptomics from Shark Bay in Australia, which harbors the largest collection of living stromatolites in the world. Objective 2 - We have expanded the analysis of the thrombolite metatranscriptome by including a diel and seasonal profile. The samples have been extracted and sequenced. Analysis of these data sets is underway Objective 3 & 4 - We plan to complete the analysis of the transcriptome data and generate a publication from this work.

Impacts
What was accomplished under these goals? Objective 1 - We have completed the sequencing of 16S rRNA gene libraries derived from a spatial profile of thrombolites, a type microbialite, isolated from The Bahamas. The data have been analyzed by my graduate student using the program QIIME and the data are currently being prepared for publication. The findings of this study clearly demonstrate a unique spatial pattern of microbes throughout the thrombolite microbial community and are distinctive from other microbialite communities. We have also examined the stable isotopic patterns of the thrombolites to provide companion data for the 16S rRNA gene data. Objective 2 - We have completed the sequencing and analysis of the metagenome and metatranscriptome of thrombolites derived from the Bahamas. We published the first metatranscriptomic paper in 2015 providing a comprehensive survey of the dominant genes expressed in the thrombolites at peak levels of photosynthesis activity. We also published a paper on another type of microbialites, known as stromatolites, and published a paper on the metagenome of this ecosystem and how closely related it is to other microbialite environments. Objective 3 - We have completed the sequencing of the transcriptome of Vibrio fischeri, the dominant symbiont of the host squid Euprymna scolopes under simulated microgravity conditions. We are currently in the process of analyzing the transcriptome libraries. Objective 4 - We have completed the sequencing of the host Euprymna scolopes transcriptome in the presence and absence of microgravity. We are in the process of analyzing that data.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Casaburi, G, AA Duscher, RP Reid, and JS Foster (2015) Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis. Environmental Microbiology DOI: 10.1111/1462-2920.13094
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mobberley, JM, CLM Khodadad, PT Visscher, RP Reid, P Hagan, JS Foster (2015) Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling. Scientific Reports 5, 12601; doi: 10.1038/srep12601
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Foster, J.S. and J.A. Lemus (2015) Developing the critical thinking skills of astrobiology students through creative and scientific inquiry. Astrobiology 15:89-99.


Progress 01/10/14 to 09/30/14

Outputs
Target Audience: There were two target audiences for the outputs of this Hatch project for this reporting period. The first audience was the astrobiology and environmental microbiology scientific communities. The second area was the space biology and host-microbe interactions scientific communities. Changes/Problems: There are no major changes to report in the nature of the science proposed. However, there are changes to the personnel. for example two of the graduate studnets have since graduated in 2014. A new graduate student Joany Babilonia has now joined the lab to work on Objectives 1 and 2; where as another graduate student Alexandrea Duscher has joined the lab and will be focused on objectives 3 and 4. What opportunities for training and professional development has the project provided? This work has provided the opportunity for the training of undergraduate and graduate students as well as a postdoctoral fellow. For example, one undergraduate and two graduate students worked on objectives 1 and 2. One of those graduate students, Jennifer Mobberley has graduated using this work as part of her PhD dissertation. In objectives 3 and 4, one undergraduate and two graduate students, and one postdoctoral fellow have work on this project. One of the graduate students, Regine Pamphile used the work from Objectives 3 and 4 as part of her MS training and graduated in 2014. The graduate and undergraduate students participating in the project presented their work at the Southeastern Branch of the American Society for Microbiology meeting in September 2014. Also the graduate students have presented their work to their department in the weekly seminar series. How have the results been disseminated to communities of interest? In addition to publications and student-led presentations, I have presented the results of this work in several invited seminars. For example, I presented the work pertaining to Objective 1 and 2 to undergraduates at the University of Florida as a a guest lecture in an Astronomy course. I also presented this work to a group of middle school students as part a summer camp program at the Center for Space education located at the Kennedy Space Center. What do you plan to do during the next reporting period to accomplish the goals? Objective 1 - We plan to submit a manuscript on these results in spring of 2015. We also plan to expand the study sites to include additional types of microbialites and also collect samples from Shark Bay in Australia, which harbors the largest collection of living stromatolites in the world. Objective 2 - we plan to expand the analysis of the thrombolite metatranscriptome by including a diel and seasonal profile. The samples are collected for this analysis and RNA extraction is underway. Objective 3 - We plan to complete the analysis of the transcriptome data and generate a publication from this work. Objective 4 - we plan to complete the transcriptome sequencing and analysis in 2015.

Impacts
What was accomplished under these goals? Objective 1 - We have completed the sequencing of 16S rRNA gene libraries derived from a spatial profile of thrombolites, a type microbialite, isolated from The Bahamas. The data have been analyzed by my graduate student using the program QIIME and the data are currently being prepared for publication. The findings of this study clearly demonstrate a unique spatial pattern of microbes throughout the thrombolite microbial community and are distinctive from other microbialite communities. Objective 2 - We have completed the sequencing and analysis of the metagenome and metatranscriptome of thrombolites derived from the Bahamas. Our findings are the first metatranscriptomic analysis of any microbialite and have been submitted for publication and provide a comprehensive survey of the dominant genes expressed in the thrombolites at peak levels of photosynthesis activity. Objective 3 - We have completed the sequencing of the transcriptome of Vibrio fischeri, the dominant symbiont of the host squid Euprymna scolopes under simulated microgravity conditions. We are currently in the process of analyzing the transcriptome libraries. Objective 4 - We have completed the simulated microgravity exposures of the host organism E. scolopes and are now optimizing the RNA extraction methodology. We anticipate to complete the sequencing portion of this project in early 2015.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Foster, JS, R. Wheeler and R. Pamphile (2014) Host-microbe interactions in microgravity: assessment and implications. Life 4(2): 250-266.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ahrendt, SR, JM Mobberley, PT Visscher, LL Koss and JS Foster (2014) Effects of elevated carbon dioxide and salinity on the microbial diversity in lithifying microbial mats. Minerals 4:145-169.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Chaturvedi, P., BA Hauser, JS Foster, E Karplus; LH Levine, JL Coutts, JT Richards, ES McLamore (2014) A multiplexing fiber optic microsensor system for monitoring spatially resolved oxygen patterns. Sensors & Actuators: B. Chemical 196:71-79.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Grant, KC, CLM Khodadad, and JS Foster (2014) Role of Hfq in an animal-microbe symbiosis under simulated microgravity conditions. International Journal of Astrobiology 13:53-61.