Progress 10/01/09 to 09/30/14
Outputs
Target Audience: Publications and presentations reached other scientists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two collaborating postdocs (one female) and one collaborating technician, 6 doctoral students (one female, 3 international), one master's student (female) and two undergraduate students received training. Eight senior participants from 6 U.S. and one Danish institutions, who are experts in microbial ecology, ecology, biochemistry, bioinformatics analyses, microsensor analyses and applied mathematics shared their knowledge with all team members The principle investigator, a mathematics faculty and two mathematics doctoral students received in-depth cross training between applied mathematics and microbiology. How have the results been disseminated to communities of interest? Publication in the peer-reviewed literature and presentation of invited talks at meetings and other institutions. What do you plan to do during the next reporting period to accomplish the goals? We will continue all efforts so long as our proposals to NSF and NASA are funded or other support can be obtained. We will submit and hopefully publish many papers related to progress to date.
Impacts
What was accomplished under these goals?
1a. We continued efforts to refine species demarcation; two related manuscripts will be submitted soon. 1b. We conducted barcode analyses of vertical distribution of Synechococcus species in winter and summer and all phototrophic taxa in summer. 1c and d. We continued efforts to cultivate and characterize multiple representatives of different Synechococcus species; two manuscripts will be submitted soon. 2a.With collaborators, we analyzed deeper-coverage metagenomes to define taxocenes and are examining their functional potentials; new metagenomes are under construction. 2b. We conducted 16S rRNA sequence barcode analysis and pigment analyses on samples collected from Mammoth hot springs in 2013; we collected samples for 2014 and analyses of these are in progress. 2c and d. With collaborators, we continued cultivation and characterization efforts and published one related paper. 2e.We performed diel collections for metatranscriptomic and metametabolomic analyses and analyses are in progress. 2f. We conducted proof-of-concept experiments on cell-sorting different phototrophic populations combined with laser ablation 13C analyses and developed a robust section of a proposal to determine a mass balance for 13C fractionation in mats. A manuscript on 13C labeling of mat proteins was published.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Slysz, G., L. Steinke, D. Ward, C. Klatt, T. Clauss, S. Purvine, S. Payne, G. Anderson,
R. Smith and M. Lipton. 2014. Automated data extraction from in situ protein stable-isotope probing studies. J. Proteome Research. 13:1200-1210.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Thiel, V., T. L. Hamilton, L. P. Tomsho, R. Burhans, S. E. Gay, S. C. Schuster, D. M. Ward, and D. A. Bryant, 2014. Draft genome sequence of a sulfide-oxidizing , autotrophic filamentous anoxygenic phototrophic bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi), GenomeA. 2: 910.
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: This work is primarily conducted for the scientific community, but is highly relevant to scientists interested in bioenergy research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? One postdoc (female), six Ph.D students (one female), one M.S. student (female), and two undergraduate students (one female) received training. The principle investigator, a mathematics faculty member, and two mathematics Ph.D. students received cross-training between applied mathematics and microbiology. How have the results been disseminated to communities of interest? Results were disseminated through scientific publications and presentations. What do you plan to do during the next reporting period to accomplish the goals? Work will be refocused on the aims of a renewed proposal that continues to address objectives on investigating geothermal microbial resources. More emphasis will be placed on understanding communities formed by anoxygenic phototrophic bacteria without cyanobacteria. Bioremediation ecology aims have been achieved and are not a part of the renewed proposal.
Impacts
What was accomplished under these goals?
Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) publication of two manuscripts describing metagenomic analyses of other Yellowstone cyanobacterial mats (Inskeep et al., 2013; Klatt et al., 2013), (ii) continued development of a manuscript based on a pilot study on stable isotope probing of mat proteins, (iii) continuation of in-depth studies on stable isotope probing of mat proteins, (iv) development of a manuscript describing diel metabolomics studies, (v) development of a manuscript on the use of barcode analyses to study the distribution, gene expression and population dynamics of Synechococcus spp., (vi) completion of barcode analyses of Synechococcus spp. regional distribution, long-term temporal change and response to disturbance, (vii) continued development of a manuscript describing multi-locus sequence analysis population genetics studies of Synechococcus spp., (viii) genomic and phenotypic characterization of cultivated Synechococcus strains of the same and different species populations, including drafting a manuscript, (ix) metabolic modeling studies of Synechococcus and Roseiflexus, (x) collaborative studies on mathematical modeling of cyanobacterial niche partitioning and physical models of the mat community, including barcode analysis of seasonal variation ofspecies in the mat and overflowing water, submission of a manuscript based on modeling niches when environmental parameters vary temporally, and development of a manuscript on cells in the effluent flow above the mat, and (xi) drafting of about three-fourths of a monograph on microbial mat community ecology. 2. Anoxygenic phototrophic bacteria. (i) Publication of two manuscripts on metagenomic analyses cited above, which include results for several Yellowstone anoxygenic phototrophic mats, (ii) publication of a paper that describes the diel transcription patterns of Chloroflexi populations (Klatt et al., 2013). (iii) 2 continued analyses of bar-code data to characterize species of all major anoxygenic phototrophic taxa and their distributions. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. Publication of a manuscript based on work completed on this project (Hamamura et al., 2013). Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Klatt, C.G., Z. Liu, M. Ludwig, M. Kuehl, S.I. Jensen, D.A. Bryant and D.M. Ward. 2013. Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a mat in a geothermal spring. ISME J. 1279-1290.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Hamamura, N., D. M. Ward and S.P. Inskeep. 2013. Effects of petroleum mixture types on soil bacterial population dynamics associated with the biodegradation of hydrocarbons in soil environments. FEMS Microbiology Ecology 85:168-178.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Inskeep, W. P., Jay, Z. J., Tringe, S. G., Herrgard, M. J., Rusch, D. B., and YNP Metagenome Progect Steering Committee and Working Group Members. (2013). The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. doi:10.3389/fmicb.2013.00067
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Klatt, C.G., W.P. Inskeep, M. Herrgard, Z.J. Jay, D.B. Rusch, S.G. Tringe, M. N. Parenteau, D.M. Ward, S.M. Boomer, D.A. Bryant and S.R. Miller. 2013. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Frontiers Microbiol. 4:article 106:1-23. Doi: 10.3389/fmicb.2013.00106.
|
Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) submission of a manuscript describing metagenomic analyses of several phototrophic mats, (ii) publication of a manuscript on metaproteomics analysis (Schaffert et al., 2012), (iii) development of a manuscript based on a pilot study on stable isotope probing of mat proteins, (iv) continuation in-depth studies on stable isotope probing of mat proteins, (v) completion of diel metabolomics studies, (vi) development of a manuscript on the use of barcode analyses to study the distribution, gene expression and population dynamics of Synechococcus spp., (vii) completion of barcode analyses of Synechococcus spp. regional distribution, long-term temporal change and response to disturbance, (viii) continued development of a manuscript describing multi-locus sequence analysis population genetics studies of Synechococcus spp., (ix) publication of book chapters on genomics and microbial community analysis (Ward et al., 2012a) and hot spring cyanobacteria (Ward et al., 2012b), (x) genomic and phenotypic characterization of cultivated Synechococcus strains of the same and different species populations, (xi) metabolic modeling studies of Synechococcus and Roseiflexus, (xii) collaborative studies on mathematical modeling of cyanobacterial niche partitioning and physical models of the mat community, including completion of continuous collection of light and temperature data, monthly collections of water and mat samples from four temperatures in two springs, and ongoing chemical and molecular analyses of these samples, (xiii) drafting of about two-thirds of a monograph on microbial mat community ecology. 2. Anoxygenic phototrophic bacteria. (i) A book chapter describing anoxygenic phototrophic mat inhabitants was published (Bryant et al., 2012). (ii) We published a paper that describes the diel transcription patterns of an uncultivated mat Chlorobi population (Liu et al., 2012) and another describing the diel transcription patterns of Chloroflexi populations was submitted, revised and resubmitted. (iii) We analyzed extensive bar-code data to characterize species of all major anoxygenic phototrophic taxa and their distributions and are in the process of obtaining additional bar-code data. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. A manuscript based on work completed on this project was submitted and is in revision. Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology. PARTICIPANTS: David M. Ward, PI, manages the project and supervises all other participants. Isaac Klapper, Dept. of Mathematics, MSU, supervised modeling work. Christian G. Klatt, Ph.D. student conducted metagenomic and metatranscriptomic analyses of Chloroflexi. Eric D. Becraft, Ph.D student, conducted bar-code analyses. Shane Nowack, Ph.D. student, conducted Synechococcus phenotypic analyses and niche partitioning modeling. Jason Wood, Ph.D. student, conducted metabolic modeling. Millie Olson, M.S. student, conducted Synechococcus cultivation and genomic analyses. Partner organizations: Pacific Northwest National Laboratory (PNNL), The Pennsylvania State University (PSU) and the University of Nebraska Medical Center (UNMC). Collaborators and contacts: Jim Fredrickson, Margie Romine, Tom Metz, Young-Mo Kim, Mary Lipton, Gordon Anderson, Gordon Sleugh (PNNL); Donald A. Bryant and Jay Liu (PSU); Laurey Steinke and Courtney Schaffert (UNMC). Training and professional development: 4 Ph.D students and one female research associate received training, as well as cross-training between microbial ecology and mathematical modeling. TARGET AUDIENCES: This work is primarily conducted for the scientific community, but is highly relevant to scientists interested in bioenergy research. During the past year we trained one female research associate. Efforts: Additional chapters of a monograph that is in development based on our microbial mat research have been drafted and revised, amounting to about two-thirds of the book. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. This year we focused on (i) completing bar-code analyses that provide a more robust demarcation of species populations and their distribution and responses to environmental change, (ii) completing metatranscriptomics analyses to conduct simultaneous gene expression work on all major functional guilds of microbial community at hourly intervals through a complete diel cycle, (iii) obtaining metabolomics results, (iv) comparative genomic and phenotypic studies of cyanobacterial species and (v) metabolic and mathematical modeling. Bar-code results are sharpening our focus on cyanobacterial species of the mat community. Metatranscriptomics and metabolomics results provided evidence of functionally unique Chlorobi and of photomixotrophic metabolisms that were previously thought to be photoautotrophic metabolisms in Chloroflexi. These observations help us understand the basis for efficient light utilization and carbon dioxide sequestration in the community and this will, in turn, help with the design of systems for bioenergy development, which we are beginning to model in silico. This multi-omics approach offers major insight into how to conduct microbial systems biology studies by providing a way to (i) identify all major mat populations, (ii) understand their functional potentials, (iii) confirm functional potential through gene expression, (iv) understand temporal gene expression patterns and (v) model interactions among community members and (vi) model the mat community physically to enable predictions about the resilience of the community that can be tested in experimental approaches. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Bryant, D.A., C.G. Klatt, N.-U. Frigaard, Z. Liu, T. Li, F. Zhao, A.M. Garcia Costas, J. Overmann and D.M. Ward. 2012. Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria, in R.L. Burnap and W. Vermaas (eds.) Functional Genomics and Evolution of Photosynthetic Systems Vol. 33, pp. 47-102. Springer, Dordrecht, The Netherlands
- Liu, Z., C.G. Klatt, M. Ludwig, D.B. Rusch, S.I. Jensen, M. Kuehl, D.M. Ward and D.A. Bryant. 2012. Candidatus Thermochlorobacter aerophilum: an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics. ISME J. 6:1869-1882.
- Schaffert, C.S. C.G. Klatt, D.M. Ward, M. Pauley and L.A. Steinke. 2012. Identification and distribution of high-abundance proteins in the Octopus Spring microbial mat community. Appl. Environ. Microbiol. 78:8481-8484.
- Ward, D.M., R.W. Castenholz and S.R. Miller. 2012. Cyanobacteria in geothermal habitats. pp. 39-63 In: Ecology of Cyanobacteria, 2nd Ed. (B.A. Whitton, ed.) Springer Science+Business Media, Heidleberg, GE.
- Ward, D.M., C.G. Klatt, J. Wood, F.M. Cohan and D.A. Bryant. 2012. Functional genomics in an ecological and evolutionary context: maximizing the value of genomes in systems biology In: Burnap RL, Vermaas W (eds) Functional Genomics and Evolution of Photosynthetic Systems. Vol. 33, pp. 1-16. Springer, Dordrecht, The Netherlands.
|
Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) publication of a manuscript describing metagenomic analyses (Klatt et al., 2011), (ii) publication of a companion manuscript describing metatranscriptomic analyses (Liu et al., 2011), (iii) collaborative studies on protein synthesis (metaproteomics), (iv) analysis of samples for a metatranscriptomics and metaproteomics study of gene expression and protein synthesis hourly over a complete diel cycle, (v) analysis of pilot study results on stable isotope probing of proteins and initiation of more in-depth studies of this type, (vi) initiation of diel metabolomics studies, (vii) publication of a manuscript describing validation of predicted ecotypes as true ecotypes through distribution studies (Becraft et al., 2011), (viii) continued analyses of bar-coding datasets to study the distribution, gene expression and population dynamics of Synechococcus spp., (ix) continued development of a manuscript describing multi-locus sequence analysis population genetics studies of Synechococcus spp., (x) analyses of full-length sequences of bacterial artificial chromosomes containing Synechococcus genomic segments, (xi) publication of a book chapter on genomics and microbial species (Ward et al., 2011), with two other book chapters in press, (xii) genomic and phenotypic characterization of cultivated Synechococcus strains of the same and different species populations, (xiii) collaborative studies on mathematical modeling of cyanobacterial niche partitioning and physical models of the mat community, including monthly collections of water and mat samples from four temperatures in two springs, initiation of chemical and molecular analyses of these samples and continuous collection of light and temperature data. 2. Anoxygenic phototrophic bacteria. A book chapter describing anoxygenic phototrophic mat inhabitants is in press. We published a description of the genome of Candidatus Chloracidobacterium thermophilum (Garcia Costas et al., 2011). A manuscript that describes the diel transcription patterns of an uncultivated mat Chlorobi population was submitted and another describing the diel transcription patterns of Chloroflexi populations is in development. We obtained extensive bar-code data to characterize species of all major anoxygenic phototrophic taxa and their distributions and are in the process of obtaining additional bar-code data. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. Publication of work. We continue to work on developing manuscripts based on work completed on this project; one manuscript is nearing submission. Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology. PARTICIPANTS: Individuals: David M. Ward, PI, manages the project and supervises all other participants. Isaac Klapper, Dept. of Mathematics, MSU, supervised modeling work. Christian G. Klatt, Ph.D. student conducted metagenomic and metatranscriptomic analyses of Chloroflexi. Eric D. Becraft, Ph.D student, conducted bar-code analyses. Shane Nowack, Ph.D. student, conducted Synechococcus phenotypic analyses and niche partitioning modeling. Millie Olson, research associate, conducted Synechococcus cultivation and genomic analyses. Partner organizations: Pacific Northwest National Laboratory (PNNL), The Pennsylvania State University (PSU) and the University of Nebraska Medical Center (UNMC). Collaborators and contacts: Jim Fredrickson, Margie Romine, Tom Metz, Young-Mo Kim, Mary Lipton, Gordon Anderson, Gordon Sleugh (PNNL); Donald A. Bryant and Jay Liu (PSU); Laurey Steinke and Courtney Schaffert (UNMC). Training and professional development: 3 Ph.D students and one female research associate received training, as well as cross-training between microbial ecology and mathematical modeling. TARGET AUDIENCES: Target Audiences: This work is primarily conducted for the scientific community, but is highly relevant to scientists interested in bioenergy research. During the past year we trained one female research associate. Efforts: During the past year, publications from our microbial mat research served as the basis for 50% of a graduate class in Microbial Ecology. Several chapters of a monograph that is in development based on our microbial mat research were reviewed by students in this class. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. This year we focused on (i) bar-code analyses that provide a more robust demarcation of species populations and their distribution and responses to environmental change and (ii) metatranscriptomics analyses to conduct simultaneous gene expression work on all major functional guilds of microbial community at hourly intervals through a complete diel cycle. Bar-code results are sharpening our focus on species populations within all functional guilds of the mat community. Metatranscriptomics results provided evidence of functionally unique Chlorobi and of photomixotrophic metabolisms that were previously thought to be photoautotrophic metabolisms in Chloroflexi and we are in the process of obtaining metabolomic and stable isotope probing data to confirm this. These observations help us understand the basis for efficient light utilization and carbon dioxide sequestration in the community and this will, in turn, help with the design of systems for bioenergy development. This multi-omics approach offers major insight into how to conduct microbial systems biology studies by providing a way to (i) identify all major mat populations, (ii) understand their functional potentials, (iii) confirm functional potential through gene expression, (iv) understand temporal gene expression patterns and (v) model interactions among community members . This year we continued efforts to construct physical models of the mat community that can be (i) refined by comparison to empirical observations and (ii) used to make predictions about the resilience of the community that can be tested in experimental approaches. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Garcia Costas, A.M. Z. Liu, L.P. Tomsho, S.C. Schuster, D.M. Ward and D.A. Bryant. 2011. Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the Phylum Acidobacteria. Environ. Microbiol. 14:177-190.
- Becraft, E.D., F.M. Cohan, M. Kuehl, S.I. Jensen and D.M. Ward. 2011. Fine-scale distribution patterns of Synechococcus ecological diversity in the microbial mat of Mushroom Spring, Yellowstone National Park. Appl. Environ. Microbiol. 77:7689-7697.
- Liu, Z., C.G. Klatt, J.M. Wood, D.B. Rusch, M. Ludwig, N. Wittekindt, L.P. Tomsho, S.C. Schuster, D.M. Ward and D.A. Bryant. 2011. Metatranscriptomic analyses of chlorophototrophs of a hot spring microbial mat. ISME J. 5:1279-1290.
- Klatt, C.G., J.M. Wood, D.B. Rusch, M.M. Bateson, N. Hamamura, J. F. Heidelberg, A. R. Grossman, D. Bhaya, F.M. Cohan, M. Kuehl, D.A. Bryant and D.M. Ward. 2011. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5:1262-1278.
- Ward, D.M., M.C. Melendrez, E.D. Becraft, C.G. Klatt, J. Wood and F.M. Cohan. 2011. Metagenomic approaches for the identification of microbial species, pp. 105-109 in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (F. J. de Bruijn, ed.) John Wiley & Sons, Inc., Hoboken, NJ.
|
Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) revision and resubmission of a manuscript describing metagenomic analyses, (ii) revision of a companion manuscript describing metatranscriptomic analyses, which is now in press, (iii) collaborative studies on protein synthesis (metaproteomics), (iv) analysis of samples for a metatranscriptomics and metaproteomics study of gene expression and protein synthesis hourly over a complete diel cycle, (v) pilot studies of stable isotope probing of proteins, (vi) publication of a manuscript describing how detection of ecologically specialized mat cyanobacterial populations (ecotypes) from individual and multiple protein-encoding genes depends on molecular resolution of the gene (Melendrez et al., 2011; online publication in 2010), (vii) development of a manuscript describing validation of predicted ecotypes as true ecotypes through distribution studies, (viii) initiation of extensive bar-coding experiments to study the distribution, gene expression and population dynamics of Synechococcus spp., (ix) development of two manuscripts describing multi-locus sequence analysis population genetics studies of Synechococcus spp., (x) initiation of full-length sequencing of bacterial artificial chromosomes containing Synechococcus genomic segments, (xi) acceptance of three book chapters and (xii) genetic characterization of Synechococcus cultures in preparation for within- and between species genomic studies. Collaborations on mathematical modeling of cyanobacterial niche partitioning continue and physical models of the mat community are in development. A new graduate student is beginning to use metagenomic and metatranscriptomic data to model organism interactions. 2. Anoxygenic phototrophic bacteria. A manuscript on the cultivation and genomic, nutritional and lipid characterization of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp. was published (van der Meer et al., 2010). A book chapter describing anoxygenic phototrophs is in press. Metagenomic assembly analyses yielded evidence of an as yet undescribed anoxygenic phototroph that is the phylogenetically deepest phototroph known to date and two novel and likely non-phototrophic mat inhabitants. We initiated an extensive bar-code experiment to characterize species of all major anoxygenic phototrophic taxa and their distributions. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. Publication of work. We continue to work on developing manuscripts based on work completed on this project; one manuscript has been drafted and is in review. Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology. PARTICIPANTS: Christian Klatt, Ph.D. student, Montana State University, Melanie Melendrez, Ph.D. student, Montana State University; Eric Becraft, Ph.D. student, Montana State University; Millie Thornton, Undergraduate student, Montana State University; Jason Wood, bioinformatics specialist, Montana State University; Isaac Klapper, Professor Department of Mathematics, Montana State University; Shane Nowack, Ph.D. student, Department of Mathematics, Montana State University; Ross Carlson, Assistant Professor, Department of Chemical Engineering, Montana State University; William P. Inskeep, Professor, LRES Department, Montana State Unviversity; Frederick M. Cohan, collaborator, Wesleyan University Douglas Rusch, collaborator, J. Craig Venter Institute Michael Kuhl, collaborator, University of Copenhagen John Heidelberg, collaborator, University of Southern California Arthur Grossman, collaborator, Carnegie Institution Devaki Bhaya, collaborator, Carnegie Institution Donald A. Bryant, collaborator, Pennsylvania State University Laurey Steinke, collaborator, University of Nebraska Medical Center, Jim Fredrickson, Pacific Northwest National Laboratory, collaborator; Mary Lipton, Pacific Northwest National Laboratory, collaborator; Paul Majors, Pacific Northwest National Laboratory, collaborator; Hailey Buberl, undergraduate student at Montana State University. TARGET AUDIENCES: Our work directly benefited the scientific community and Yellowstone National Park administrators. We trained two undergraduate students and five graduate students at MSU (plus many others at collaborating institutions), three of them female, one Hispanic. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. This year we used metagenomic assembly methods to discover two novel putatively non-phototrophic members of the mat community. Awareness of the existence of these organisms will drive their recovery in culture, which should lead, in turn, to major insights in mat decomposition processes. We used metatranscriptomics analyses to conduct simultaneous gene expression work on all major functional guilds of microbial community at hourly intervals through a complete diel cycle. This approach offers major insight into how to conduct microbial systems biology studies by providing a way to (i) identify all major mat populations, (ii) understand their functional potentials, (iii) confirm functional potential through gene expression, (iv) understand temporal gene expression patterns and (v) model interactions among community members . This year we initiated attempts to construct physical models of the mat community that can be (i) refined by comparison to empirical observations and (ii) used to make predictions about the resilience of the community that can be tested in experimental approaches. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Melendrez, M.C., R.K. Lange, F.M. Cohan and D.M. Ward. 2011. Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat. Appl. Environ. Microbiol. 77:1359-1367 (published online in 2010).
- van der Meer M.T.J., C.G. Klatt, J. Wood, D.A. Bryant, M.M. Bateson, L. Lammerts, S. Schouten, J. S. Sinninghe Damste, M.T. Madigan and D.M. Ward. 2010. Cultivation and genomic, nutritional and lipid biomarker characterization of Roseiflexus strains closely related to predominant in situ populations inhabiting Yellowstone hot spring microbial mats. J. Bacteriol. 192:3033-3042.
|
Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) development of a manuscript describing metagenomic analyses, (ii) development of a companion manuscript describing metatranscriptomic analyses, (iii) collaborative studies on protein synthesis (metaproteomics), (iv) collection and analysis of samples for a metatranscriptomics and metaproteomics study of gene expression and protein synthesis hourly over a complete diel cycle, (v) pilot studies of stable isotope probing of proteins, (vi) development of three manuscripts describing ecologically specialized mat cyanobacterial populations (ecotypes) from individual and multiple protein-encoding genes, (vii) initiation of a manuscript describing validation of predicted ecotypes as true ecotypes in distribution, population dynamics and gene expression studies, and (viii) development of two book chapters, one in review. We are genetically characterizing Synechococcus cultures in preparation for within- and between species genomic studies. Collaborations on mathematical modeling of cyanobacterial niche partitioning continue; one resulted in a publication (Taffs et al., 2009). 2. Anoxygenic phototrophic bacteria. A manuscript on the cultivation and genomic, nutritional and lipid characterization of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp. is in review. A book chapter describing anoxygenic phototrophs is in review. Metagenomic assembly analyses yielded evidence of an as yet undescribed anoxygenic phototroph that is the phylogenetically deepest phototroph known to date. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. Publication of work. We continue to work on developing manuscripts based on work completed on this project. Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology. PARTICIPANTS: Christian Klatt, Ph.D. student, Montana State University Melanie Melendrez, Ph.D. student, Montana State University; Eric Becraft, Ph.D. student, Montana State University; Rachel Lange, Undergraduate student, Montana State University; Jason Wood, bioinformatics specialist, Montana State University; Isaac Klapper, Professor Department of Mathematics, Montana State University; Shane Nowack, Ph.D. student, Department of Mathematics, Montana State University; Ross Carlson, Assistant Professor, Department of Chemical Engineering, Montana State University; William P. Inskeep, Professor, LRES Department, Montana State Unviversity; Frederick M. Cohan, collaborator, Wesleyan University Douglas Rusch, collaborator, J. Craig Venter Institute Michael Kuhl, collaborator, University of Copenhagen John Heidelberg, collaborator, University of Southern California Arthur Grossman, collaborator, Carnegie Institution Devaki Bhaya, collaborator, Carnegie Institution Donald A. Bryant, collaborator, Pennsylvania State University Laurey Steinke, collaborator, University of Nebraska Medical Center, Jim Fredrickson, Pacific Northwest National Laboratory, collaborator; Mary Lipton, Pacific Northwest National Laboratory, collaborator. TARGET AUDIENCES: Our work directly benefited the scientific community and Yellowstone National Park administrators. We are trained one undergraduate student and four graduate students at MSU (plus many others at collaborating institutions), two of them female, one Hispanic. We hosted a workshop that trained several tens of students and faculty at Montana State University and elsewhere in the US and abroad how to think about microbial species and speciation. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. This year we used metagenomic assembly methods to discover the phylogenetically deepest phototroph. Awareness of the existence of this organism will drive its recovery in culture, which should lead, in turn, to major insights in the evolution of photosynthesis. We used metatranscriptomics analyses to conduct simultaneous gene expression work on all major functional guilds of microbial community. This approach offers major insight into how to conduct microbial systems biology studies. This year we also discovered that recombination has not interfered with the molecular detection of ecological species. This advances knowledge of how recombination is involved in the evolution of microbial diversity, a topic of considerable debate and misunderstanding in microbiology. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Taffs, R. J.E. Aston, K. Brileya, Z. Jay, C.G. Klatt, S. McGlynn, N. Mallette, S. Montross, R. Gerlach, W.P. Inskeep, D.M Ward and R.P. Carlson (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study BMC Systems Biology 3:114 doi: 10.1186/1752-0509-3-114
|
Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial species. Molecular analyses of hot spring microbial mats continued with (i) construction and analyses of metagenomic assemblies, (ii) diel variations in expression of cyanobacterial genes for nitrogen fixation, photosynthesis and fermentation (Steunou et al., 2008), (iii) collaborative studies on community gene expression (metatranscriptomics) and protein synthesis (metaprotomics), (iv) prediction of ecologically specialized mat cyanobacterial populations (ecotypes) from individual and multiple protein-encoding genes, and (v) validation of predicted ecotypes as true ecotypes in distribution, population dynamics and gene expression studies. We are increasing our Synechococcus culture collection in preparation for within- and between species genomic studies. We have initiated collaborative work on mathematical modeling of cyanobacterial niche partitioning. 2. Anoxygenic phototrophic bacteria. We are finalizing a manuscript on the cultivation and genomic, nutritional and lipid characterization of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp. We published on the unique autotrophic pathway in Roseiflexus spp. (Klatt et al., 2007). In collaborative work we obtained the genomes of two Yellowstone Chloroflexus strains and the newly discovered Candidatus Chloracidobacterium thermophilum. Metagenomic assembly analysis yielded further evidence of an as yet uncultivated green sulfur bacterial inhabitant in the mat. We submitted a paper on modeling microbial interactions in the mat from genomic data. We have obtained and initiated analysis of metagenomic sequences for several other Yellowstone mats containing anoxygenic phototrophs. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. Bioremediation Ecology. 1. Publication of work. We published a paper on temperature effects on alkane-degrading bacteria (Hamamura et al., 2008). Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology. PARTICIPANTS: Christian Klatt, Ph.D. student, Montana State University Melanie Melendrez, Ph.D. student, Montana State University Eric Becraft, Ph.D. student, Montana State University Rachel Lange, Undergraduate student, Montana State University Jason Wood, bioinformatics specialist, Montana State University Isaac Klapper, Department of Mathematics, Montana State University Shane Nowack, Ph.D. student, Department of Mathematics, Montana State University Frederick M. Cohan, collaborator, Wesleyan University Douglas Rusch, collaborator, J. Craig Venter Institute Michael Kuhl, collaborator, University of Copenhagen John Heidelberg, collaborator, University of Southern California Arthur Grossman, collaborator, Carnegie Institution Devaki Bhaya, collaborator, Carnegie Institution Donald A. Bryant, collaborator, Pennsylvania State University Laurey Steinke, collaborator, University of Nebraska Medical Center TARGET AUDIENCES: Our work directly benefited the scientific community and Yellowstone National Park administrators. We are training one undergraduate student and four graduate students at MSU (plus many others at collaborating institutions), two of them female, one Hispanic. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Hamamura, N., M. Fukui, D.M. Ward and W.I. Inskeep. 2008. Assessing soil microbial populations responding to crude-oil amendment at different temperatures using phylogenetic, functional gene (alkB) and physiological analyses. Env. Sci. Technol. 42:7580-7586.
- Klatt, C.G., D.A. Bryant and D.M. Ward. 2007. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ. Microbiol. 9:2067-2078.
- Steunou, A.-S., S.I. Jensen, E. Brecht, E.D. Becraft, M. M. Bateson, O. Kilian, D. Bhaya, D. M. Ward, , J.W. Peters, A.R. Grossman and M. Kuhl. 2008. Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. ISME J. 2:364-378.
|
Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We published analyses of hot spring microbial mat photic-layer metagenomic DNA sequences and genomes of several genetically relevant mat isolates, describing (i) native Synechococccus populations ecologically distinct from the isolates (e.g., capable of Fe+2 uptake; Bhaya et al., 2007) and (ii) novel anoxygenic phototrophs, including the first phototrophic acidobacterium (Bryant et al., 2007). We are developing a manuscript describing metagenomic analysis of mat community structure and providing evidence suggesting that gene exchange and genome organization parallel relatedness (Klatt et al., in prep.). This theory-independent approach is being compared to a theory-based, high-resolution population genetics analysis of ecologically specialized mat populations (ecotypes) (Ward et al., 2008). We published a theory-based evolutionary simulation method to identify putative ecotypes from genetic variation (Koeppel et
al., 2008). We progressed with (i) analyses suggesting that these putative ecotypes have unique ecological distributions, as expected of true ecotypes (species) and (ii) development of cultivation-independent multi-locus population genetics methods for ecotype detection. We published on Synechococcus in situ gene expression over a full diel cycle (Steunou et al., in press). 2. Organic geochemical studies: We are preparing a manuscript describing the cultivation and characteristics of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp. We completed the Roseiflexus genome and published on its unique autotrophic pathway (Klatt et al., 2007). We are obtaining genomes of several other related organisms, as well as the novel acidobacterial phototroph. We initiated metagenomic analysis of mat layers beneath the photic zone and mats in sulfidic hot springs. We published on novel archaeal and bacterial lipids in hot spring microbial communities (Schouten et al., 2007). 3.
Geographic variation among cyanobacteria: done. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. 4. Microbial diversity in acid thermal areas. Done. Bioremediation Ecology. 5. Competitive fitness of phenanthrene-degrading bacteria. We published on how surface properties and sorption characteristics may control competitive fitness of these bacteria (Colores et al., 2007). 6. Mixture complexity effects on contaminant-degrading microbial populations. A manuscript on temperature effects on hydrocarbon-degrading populations is in review (Hamamura et al., submitted). Manuscripts in preparation describe (i) functional gene analysis of hydrocarbon-degrading populations and (ii) how soil hydrocarbon-degrading populations respond to different contaminant mixture types.
Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology.
PARTICIPANTS: Ward Lab at Montana St. Univ.: Lab head: David M. Ward, ; Postdocs: Greg Colores, Natsuko HamamuraPh.D. students: Christian G. Klatt, Melanie Melendrez,Eric Becraft; Undergraduate students: Rachelle Lange, Jason Wood; Lab manager: Mary Bateson; other MSU participants: Bill Inskeep, John Peters, Eric Brecht Wesleyan Univ. collaborators: Fred Cohan, head of lab; Ph.D. students: Alex Koeppel; M.S. Student: Liz Perry; Carnegie Inst. (Stanford) collaborators: lab heads: Devaki Bhaya, Arthur Grossman; Postdocs: Anne Steunou, Natasha Khuri, Olli Killian Univ. So. Cal. collaborator: Lab head: John Heidelberg Univ. Copenhagen collaborators: Lab head: Michael Kuhl; Ph.D. student: Sheila Jensen Univ. Hokkaido collaborator: Manabu Fukui Penn. St. Univ. collaborators: Lab head: Don Bryant; Ph.D. student: Amaya Garcia Costas Roy. Netherlands Inst. Sea Res. collaborators: Lab heads: Stephan Schouten, Jaap Sinninghe Damste; Postdoc: Marcel van der Meer
TARGET AUDIENCES: Our target audiences are microbial ecologists interested in any natural or human-influenced microbial community.
PROJECT MODIFICATIONS: None
Impacts
Our Geothermal Microbial Resource findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems. A specific example is the discovery of the first phototrophic member of the Acidobacteria Kingdom in Domain Bacteria, a relatively newly described and poorly characterized group of mainly soil bacteria. Our work continues to significantly influence the many investigators using molecular methods to describe microbial diversity in numerous habitats. All are seeking to understand how molecular variation correlates to ecologically meaningful variation. In this regard, our theory-based evolutionary simulation for predicting ecotypes has already been applied to several different microbial taxa, including Bacillus and Legionella. Our comparison of these new methods to genomic and metagenomic methods that have become popular in microbial community analysis will help guide others to better understand the limits of genomic
technologies. Our Bioremediation Ecology findings continue to inform us of how specifically adapted microorganisms act as the underpinnings of microbial degradation of different kinds of contaminant mixtures in different kinds of environments. We are demonstrating the kinds of environmental parameters that influenced the evolution and thus control the ecology of differently adapted contaminant-degrading bacteria.
Publications
- Bhaya, D., A.R. Grossman, A.-S. Steunou, N. Khuri, F.M. Cohan, N.Hamamura, M.C. Melendrez, W. Nelson, M.M. Bateson, D.M. Ward and John F. Heidelberg. 2007. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. ISME J. 1:7-3-713.
- Bryant, D.A.,A M. Garcia Costas, J. A. Maresca, A.Gomez Maqueo Chew, C.G. Klatt, M.M. Bateson, L.J. Tallon, J. Hostetler, W.C. Nelson, J.F. Heidelberg and D.M. Ward. 2007 Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 317:523-526.
- Colores, G.M., D.M. Ward and W.P. Inskeep. 2007. Competitive fitness of isolates enriched on phenanthrene sorbed to model phases. Appl. Environ. Microbio. 73:4074-4077.
- Hamamura, M. Fukui, D.M. Ward, and W.P. Inskeep. 2008.Assessing soil microbial populations responsible for n-alkane degradation at different temperatures using 16S rRNA and alkB gene analysis and cultivation. (submitted)
- Klatt, C.G., D.A. Bryant and D.M. Ward. 2007. Comparative genomics provides evidence for the 3-hydroxypropionate zutotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ. Microbiol. 9:2067-2078.
- Koeppel, A, E.B. Perry, J. Sikorski, D. Krizanc, A. Warner, D.M. Ward, A.P. Rooney, E. Brambilla, N. Connor, E. Nevo, R.M. Ratcliff, and F.M. Cohan. 2008 Identifying the Fundamental Units of Bacterial Diversity:A Paradigm Shift to Incorporate Ecological Diversification into Bacterial Systematics, Proc. Natl. Acad. Sciences, USA) 105:2504-2509.
- Schouten, S., M. T. J. van der Meer, E. C. Hopmans, W.I.C. Rijpstra A.L. Reysenbach, D.M. Ward and J.S. Sinninghe Damste. 2007. Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of Yellowstone National Park. Appl. Environ. Microbiol. 73: 6181-6191.
- Steunou, A.-S., S.I. Jensen, E. Brecht, E.D. Becraft, M.M. Bateson, O. Kilian, D. Bhaya, D. M. Ward, J.W. Peters, A.R. Grossman and M. Kuhl. 2008. Regulation of nif gene expression and the energetics of cyanobacterial N2 fixation over the diel cycle in a hot spring microbial mat ISME J. (in press)
- Ward, D.M., F.M. Cohan, D. Bhaya, J.F. Heidelberg, M. Kuhl and A. Grossman. 2008. Genomics, environmental genomics and the issue of microbial species. Nature Heredity 100:207-219.
|
Progress 01/01/06 to 12/31/06
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We published on temperature and light adaptations of genetically relevant Synechococcus isolates predominating in Yellowstone hot spring mats (Allewalt et al., 2006). We conducted bioinformatic analysis of genomes of two Synechococcus isolates and metagenomic sequences on four mats they inhabit, discovering (i) native Synechococccus populations ecologically distinct from the isolates (e.g., capable of Fe+2 uptake; Bhaya et al., submitted; 2007 report) and (ii) novel anoxygenic phototrophs (Bryant et al., submitted; 2007 report). These databases provide a foundation for theory-based, high-resolution population genetics analysis of ecologically specialized mat populations (ecotypes) (Ward et al., submitted; 2007 report). We developed (Cohan et al., in prep.; next year's report) and validated (Ward et al., 2006) a single-locus method for this purpose. We progressed with development of cultivation-independent
multi-locus population genetics methods for ecotype detection. We published in situ gene expression results indicating that Synechococcus shifts between daytime photosynthesis and nighttime fermentation and nitrogen fixation (Steunou et al., 2006). We published invited reviews on microbial species concepts (Ward, 2006, 2007). 2. Organic geochemical studies: We published on a diel rhythm in Synechococcus spp. of daytime polyglucose synthesis and nighttime fermentation and demonstrated that these sugars are isotopically heavy enough to account for heavy Roseiflexus spp. cell components via uptake of Synechococcus fermentation products (van der Meer et al., 2007). We are preparing a manuscript describing the cultivation and characteristics of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp. We completed the Roseiflexus genome and performed bioinformatics analysis revealing its unique autotrophic pathway (Klatt et al., in press; 2007 report). 3. Geographic variation
among cyanobacteria: done. Results of our work on geothermal microbial resources are generally important as they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, thus the nature of microbial species, and how they control community function. 4. Microbial diversity in acid thermal areas. Done. Bioremediation Ecology. 5. Competitive fitness of phenanthrene-degrading bacteria. A manuscript (Colores et al., submitted; 2007 report) showing that surface properties and sorption characteristics may control competitive fitness is in revision. 6. Mixture complexity effects on contaminant-degrading microbial populations. We published a manuscript on how hydrocarbon-degrading populations in different soils respond to crude oil contamination (Hamamura et al., 2006). Manuscripts in preparation describe (i) functional gene analysis of hydrocarbon-degrading populations and (ii) how soil hydrocarbon-degrading populations respond to different
contaminant mixture types. Our bioremediation work is generally important as it puts an ecological underpinning to applied microbial ecology.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Allewalt, J.P., M.M. Bateson, N.P. Revsbech, K. Slack and D.M. Ward. 2006. Effect of temperature and light on growth and photosynthesis of Synechococcus isolates typical of those predominating in the Octopus Spring microbial mat community. Appl. Environ. Microbiol. 72:544-550.
- Hamamura, N., S.H. Olson, D.M. Ward and W.P. Inskeep. 2006. Microbial population dynamics associated with crude-oil biodegradation in diverse soils. Appl. Environ. Microbiol. 72:6316-6324.
- Steunou, A.-S., D. Bhaya, M. M. Bateson, M.C. Melendrez, D. M. Ward, E. Brecht, J.W. Peters, M. Kuhl and A.R. Grossman. 2006. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats, Proc. Natl. Acad. Sci., U.S.A 103:2398-2403
- van der Meer, M.T.J., S. Schouten, J.S. Sinninghe Damste and D.M. Ward 2007. Impact of carbon metabolisms on 13C signatures of cyanobacteria and green nonsulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA) Environ. Microbiol. 9:482-491
- Ward, D.M., M.M. Bateson, M.J. Ferris, M. Kuhl, A. Wieland, A. Koeppel and F.M. Cohan. 2006. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Phil. Trans. Royal Soc., London (Ser. B) 361:1997-2008.
- Ward, D.M. 2006. Microbial diversity in natural environments: focusing on fundamental questions. Antonie Van Leeuwenhoek 90:309-324.
- Ward, D.M. 2006. A macrobiological perspective on microbial species. Microbe 1:269-278.
|
Progress 01/01/05 to 12/31/05
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We published work on temperature and light adaptations of genetically relevant Synechococcus isolates predominating in Yellowstone hot spring mat communities (Allewalt et al., 2006 to be included in 2006 report). The genomes of two of these isolates were completed in collaboration with The Institute for Genome Research (www.tigr.org) and metagenomic sequence databases on four mat samples were constructed. These databases provide a foundation for theory-based, high-resolution population genetics analysis of ecologically specialized mat cyanobacterial populations. We are developing cultivation-independent single- and multi-locus sequence typing methods for this purpose with colleagues at Wesleyan Univ. (Ward and Cohan, 2005). The genomes have already enabled studies of temporal variation in in situ expression of nitrogen fixation genes (previously unknown in high-temperature Synechococccus), photosynthesis
and fermentation genes (Steunou et al., 2006 to be reported in 2006). We enhanced our work on 16S rRNA and 16S-23S rRNA internal transcribed spacer (ITS) sequence variation at different temperature sites in two hot spring microbial mats and are developing a manuscript based on theory-based analysis of these data to reveal ecotypes. 2. Organic geochemical studies: With colleagues at the Royal Netherlands Inst. of Ocean Res. we reported diel changes in photosynthetic physiologies of mat organisms (van der Meer et al., 2005), and also with So. Illinois Univ. collaborators, we are developing manuscripts on (i) further analysis of stable carbon isotopes of lipids and carbohydrates in mats and cultivated cyanobacteria and (ii) characteristics of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp.. With a colleague at Penn St. Univ. we completed analysis of the Roseiflexus genome. 3. Geographic variation among cyanobacteria: work completed. Results of our work on
geothermal microbial resources are of general importance in that they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, and thus the nature of microbial species and how they control community function. 4. Microbial diversity in acid thermal areas. Work completed. Bioremediation Ecology. 5. Competitive fitness of phenanthrene-degrading bacteria. Our completed study showing that both surface properties and sorption characteristics may control competitive fitness is in an advanced stage of preparation for publication. 6. Mixture complexity effects on contaminant-degrading microbial populations. We published a manuscript on hydrocarbon-degrading populations in an acid soil from Yellowstone N.P. (Hamamura et al., 2005); three more manuscripts in preparation describe how these populations vary in different soils and with different contaminant mixture types. We continue attempts to publish two manuscripts showing how changes in
mixture complexity during biodegradation affect microbial community composition.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Ward, D.M. and F.M. Cohan. 2005. Microbial diversity in hot spring cyanobacterial mats: Pattern and Prediction. pp.185-201 in W.P. Inskeep and T.R. McDermott (eds.) Geothermal Biology and Geochemistry in Yellowstone National Park, Thermal Biology Institute, Montana State University, Bozeman, MT.
- Van der Meer, M.T.J., S. Schouten, M.M. Bateson, U. Nubel, A. Wieland, M. Kuhl, J.W. deLeeuw, J. S. Sinninghe Damste and D.M. Ward. 2005. Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park. Appl. Environ. Microbiol. 71:3978-3986. [cover photo]
- Hamamura, N. S.H. Olson, D.M. Ward and WP. Inskeep. 2005. Diversity and Functional Analysis of Bacterial Communities Associated with Natural Hydrocarbon Seeps in Acidic Soils at Rainbow Springs, Yellowstone National Park. Appl. Environ. Microbiol. 71:5943-5950.
|
Progress 01/01/04 to 12/31/04
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We progressed toward our goal of developing a manuscript reporting the results of 2-dimensional analysis of 16S rRNA and 16S-23S rRNA internal transcribed spacer (ITS) sequence variation at 4 temperature sites in a hot spring microbial mat. Results suggest that ecologically distinct populations may have variable genetic relatedness; some may not even be detected by ITS variation. We completed work on temperature and light adaptations of genetically relevant Synechococcus isolates from the mat (Allewalt, 2004; Allewalt et al., submitted). The genomes of two of these isolates were completed with the Institute for Genome Research to provide a basis for high-resolution population genetics analysis of ecologically specialized mat cyanobacterial populations. We are developing cultivation-independent multi-locus sequence typing methods for this purpose with colleagues at Wesleyan Univ. The genomes have already
enabled ed studies of in situ gene expression by collaborators at The Carnegie Inst. (Stanford). 2. Organic geochemical studies: With colleagues at the Neth. Inst. of Ocean Res. on photosynthetic physiologies of mat organisms we have progressed with acceptance of another manuscript (van der Meer et al., in press) and further analysis of stable carbon isotopes of lipids and carbohydrates in mats and cultivated cyanobacteria. With a colleage at Penn St. Univ. we have begun to analyze the genome of the main filamentous anoxygenic phototroph of the mat, Roseiflexus spp., which we have successfully cultivated. 3. Geographic variation among cyanobacteria: We completed our work on this objective by publishing an invited minireview (Papke and Ward, 2004). Results of our work on geothermal microbial resources are of general importance in that they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, and thus the nature of microbial
species. 4. Microbial diversity in acid thermal areas. We continue attempts to publish results describing substantial diversity among algae in this system. Bioremediation Ecology. 5. Competitive fitness of phenanthrene-degrading bacteria. Our completed study showing that both surface properties and sorption characteristics may control competitive fitness is in an advanced stage of preparation for publication. 6. Mixture complexity effects on contaminant-degrading microbial populations. We have submitted a manuscript on hydrocarbon-degrading populations in an acid soil from Yellowstone N.P. (Hamamura et al., submitted) with two more manuscripts in preparation describing how these populations vary in different soils. Experiments on how these populations vary with contaminant mixture type are in progress. We continue attempts to publish two manuscripts showing how changes in mixture complexity during biodegradation affect microbial community composition.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Allewalt, J.P. 2004. Temperature and light adaptations of Synechococcus isolates from a hot spring microbial community. M.S. thesis, Dept. of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT.
- Papke, R.T. and D.M. Ward. 2004. The importance of physical isolation in microbial evolution. FEMS Microbiology Ecology 48:293-303.
|
Progress 01/01/03 to 12/31/03
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We are completing publication of the results of 2-dimensional analysis of 16S-23S rRNA internal transcribed spacer (ITS) sequences cloned from a hot spring cyanobacterial mat. Ferris et al. (2003) describe the discovery of ITS-defined ecotypes not discerned by 16S rRNA sequence in different light microenvironments. Another paper will report results on variation at 4 temperature sites, which suggest that ecologically distinct populations may have variable genetic relatedness; some may not even be detected by ITS variation. We also cultivated from the mat numerous genetically relevant Synechococcus isolates; different genotypes have different upper temperature limits and growth rates at low and high light intensity, likely explaining their distribution along thermal and light gradients. New grants fund continued studies of how genetic diversity relates to ecological diversity, capitalizing on sabbatical
contacts that provide a theoretical framework and collaborations developed with cyanobacterial physiologists and genomicists. One grant enables us to pursue a new objective, based on our renewed MAES support, organic geochemical studies of photosynthetic physiologies of mat organisms (e.g., van der Meer et al., 2003). 2. Geographic variation among cyanobacteria: Papke et al. (2003) showed how geographic isolation influences hot spring cyanobacterial diversity. A minireview on geographic isolation in bacterial diversification is in revision. Results of our work on geothermal microbial resources are of general importance in that they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, and thus the nature of microbial species. 3. Microbial diversity in acid thermal areas. Sheehan et al. (2003a and b) and describe diversity among protozoal inhabitants of an acid thermal mat system and Ferris et al. (2003) describes the use of
sulfide microsensors, enrichments cultures and analysis of sulfite reductase genes to demonstrate sulfate reduction in the same system; we continue attempts to publish results describing substantial diversity among algae in this system. Bioremediation Ecology. 4. Competitive fitness of phenanthrene-degrading bacteria. Our completed study showing that both surface properties and sorption characteristics may control competitive fitness is in preparation for publication. 5. Mixture complexity effects on contaminant-degrading microbial populations. We continue attempts to publish two manuscripts showing how changes in mixture complexity during biodegradation affect microbial community composition. Our EPA award has sponsored development of PCR primers targeting phylogenetically distinct functional genes for analyzing the diversity of alkane and aromatic hydrocarbon-degrading bacteria. The primers have been tested on pure cultures and on artificially contaminated soils. New personnel will
use these primers to investigate how mixture type, soil type and changing mixture complexity during biodegradation affect contaminant-degrading community members.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Sheehan, K.B., M.J. Ferris and J.M. Henson. 2003. Detection of Naegleria sp. in a thermal, acidic stream in Yellowstone National Park. J. Eukaryot. Microbiol. 50:263-265.
- Ferris, M.J., Kuehl, M., Wieland, A. and Ward, D.M. 2003. Cyanobacterial ecotypes in different optical microenvironments of a 68 C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation. Appl. Environ. Microbiol. 69, 2893-3898.
- Ferris, M.J., T.S. Magnuson, J.A. Fagg, R. Thar, M. Kuehl, K.B. Sheehan and J.M. Henson. 2003. Microbially mediated sulphide production in a thermal, acidic algal mat community in Yellowstone National Park. Environ. Microbiol. 5:954-960.
- Papke, R.T., Ramsing, N.B., Bateson, M.M. and Ward, D.M. 2003. Geographical isolation in hot spring cyanobacteria. Environ. Microbiol., 5, 650-659.
- Sheehan, K.B., J.A. Fagg, M.J. Ferris and J.M. Henson. 2003. PCR detection and analysis of the free-living amoeba Naegleria in hot springs in Yellowstone and Grand Teton National Parks. Appl. Environ. Microbiol. 69:5914-5918.
- van der Meer , M.T.J., S. Schouten, J.S. Sinninghe Damste, J.W. de Leeuw and Ward, D.M.. 2003. Compound-specific isotope fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot-spring microbial mats. Appl. Environ. Microbiol. 69:6000-6006.
|
Progress 01/01/02 to 12/31/02
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We are publishing the completed results of two-dimensional analysis of 16S-23S rRNA internal transcribed spacer (ITS) sequences cloned from a hot spring cyanobacterial mat. One in press paper describes the discovery of ITS-defined ecotypes not discerned by 16S rRNA sequence in different light microenvironments. Another paper is planned on 2-dimensional 16S rRNA and ITS variation at 4 temperature sites in the mat. The second study suggests that ecologically distinct populations may have variable genetic relatedness; some may not even be detected by ITS variation. We have also cultivated from the mat numerous Synechococcus isolates, which are genetically relevant. We are purifying these isolates in advance of phenotypic studies of their temperature and light adaptations. Proposals were submitted to fund continued studies of how genetic diversity relates to ecological diversity, capitalizing on sabbatical
contacts that provide a theoretical framework and collaborations developed with cyanobacterial physiologists and genomicists. We published a study of diversity and distribution of mat green nonsulfur-like bacteria. 2. Geographic variation among cyanobacteria: A paper based on our results indicating that geographic isolation influences hot spring cyanobacterial diversity is in press. A minireview on geographic isolation in bacterial diversification will be submitted soon. Results of our work on geothermal microbial resources are of general importance in that they influence how microbiologists think about the relationship between genetic diversity and ecological diversity, and thus the nature of microbial species. 3. Microbial diversity in acid thermal areas. We have detected substantial diversity among algal and protozoal inhabitants of an acid thermal mat system. Two manuscripts describing these results have been submitted. We have also used sulfide microsensors, enrichments cultures
and analysis of sulfite reductase genes to demonstrate sulfate reduction in the same system. A manuscript describing these results has also been submitted. Bioremediation Ecology. 4. Competitive fitness of phenanthrene-degrading bacteria. Our completed study showing that both surface properties and sorption characteristics may control competitive fitness is in preparation for publication. 5. Mixture complexity effects on contaminant-degrading microbial populations. Two manuscripts showing how changes in mixture complexity during biodegradation affect microbial community composition are in preparation. A new EPA award has sponsored development of a set of PCR primers targeting phylogenetically distinct functional genes for analyzing the diversity of alkane and aromatic hydrocarbon-degrading bacteria. The primers and hybridization conditions are being tested on pure cultures. New personnel were recruited to use these primers to investigate how mixture type, soil type and changing
mixture complexity during biodegradation affect contaminant-degrading community members.
Impacts
Our findings continue to reveal the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a basis for understanding the significance of molecular diversity. Our bioremediation ecology findings continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading bacteria.
Publications
- Papke, R.T. 2002. Biogeography of thermophilic cyanobacteria and the importance of isolation to the evolution of microorganisms. Ph.D. thesis, Montana State Univ., Bozeman, 75 p.
- Nubel, U., M.M. Bateson, V. Vandieken, A. Wieland, M. Kuhl and D.M. Ward. 2002. Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats. Appl. Environ. Microbiol. 68: 4593-4603.
- Ferris, M.J., M. Kuhl, A. Wieland and D.M. Ward. 2003. Cyanobacterial ecotypes in different optical microenvironments of a 68 degrees C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation, Appl. Environ. Microbiol. 69: (in press)
|
Progress 01/01/01 to 12/31/01
Outputs
Geothermal Microbial Resources. 1. Cyanobacterial adaptations: We are completing two-dimensional distribution studies with analysis of cloned 16S-23S rRNA intervening transcribed spacer (ITS) sequences for temperatures where no vertical variation is found at the 16S rRNA locus. ITS analysis revealed evidence of distinct genetic populations with identical 16S rRNA sequences at different depths, or, at other temperatures, physiologically distinct populations that exhibit no difference at either 16S rRNA or ITS loci. Several manuscripts reporting microsensor, DGGE and cloning/sequencing data are in preparation. We are genotyping greater than 100 Synechococcus isolates and have found that most have relevant genotypes compared to those found in situ. Phenotypic studies will soon be initiated. I conducted a sabbatical leave to learn principles of evolutionary ecology, population genetics, and genomics. A proposal has been developed to fund future work utilizing the
knowledge gained to identify and characterize closely related ecotypes at very high resolution. 2. Geographic variation among cyanobacteria: Collated data from our global diversity study suggest strongly that geographic isolation is important to divergence of hot spring cyanobacteria. Manuscripts are completed and will soon be submitted. 3. Microbial diversity in acid thermal areas: A manuscript on algal molecular variation has been submitted. Another on sulfate reduction is in preparation. Bioremediation Ecology: 4. Studies of competitive fitness of phenanthrene-degrading bacteria have been completed. Results suggest that the type of surface as well as sorptive properties of model solid phases may be involved in selection of specific most-fit populations. A manuscript is in preparation. 5. Manuscripts showing how mixture complexity effects on microbial community composition are nearing completion. A new EPA award was funded to initiate future work on (i) how various real contaminant
mixtures affect selection of contaminant-degrading bacteria in soil, using functional gene probes to assay contaminant degrader diversity, and (ii) linking contaminant-degrading function with phylogenetic molecular analysis. 6. Studies on the effect of organic matter/contaminant mixture interactions on microbial community complexity, based on use of a single solid phase with different porosity to isolate sorption as a variable, are nearing completion.
Impacts
Our findings have and will continue to acquaint microbiologists with the enormous diversity of highly adapted microorganisms in natural thermal systems and their biotechnological potential, providing a theoretical basis for understanding the significance of molecular diversity. Our bioremediation ecology findings have and will continue to demonstrate what controlled the evolution and thus controls the ecology of adapted contaminant-degrading populations.
Publications
- Ferris, M.J., Nold, S.C., Santegoeds, C.M. and Ward, D.M. 2001. Examining bacterial population diversity within the Octopus Spring microbial mat community. p. 51-64. In A.-L. Reysenback, M. Voytek and R. Mancinelli(eds.) Thermophiles: Biodiversity, ecology and evolution. Kluwer Academic/Plenum Publishers, NY.
- Ward, D.M., Bateson M.M. and deLeeuw, J.W. 2001. Use of 16S rRNA, lipid and naturally preserved components of hot spring mats and microorganisms to help interpret the record of microbial evolution. p. 167-181. In A.-L. Reysenback, M. Voytek and R. Mancinelli(eds.) Thermophiles: Biodiversity, ecology and evolution. Kluwer Academic/Plenum Publishers, NY.
- Kern, E.A. 2001. Investigation of microbial population biology during the degradation of organic contaminant mixtures. Ph.D. Dissertation, Montana State Univ., Bozeman. 121 p.
|
Progress 01/01/00 to 12/31/00
Outputs
Geothermal Microbial Resources--1. Cyanobacterial adaptations: Vertical distribution paper published. To study two dimensional distribution in Mushroom Sp. mat, Yellowstone Natl. Park, we continue to analyze in situ microsensor data and to perform denaturing gradient gel electrophoresis analysis of 16S rRNA-based diversity. We recovered and are genotyping tens of new Synechococcus isolates and piloted microsensor analysis of photosynthesis rates in isolate biofilms and colonies. I was awarded a sabbatical leave to pursue objectives related to population genetics studies that we hope to conduct on these isolates as well as on large DNA segments cloned from mat Synechococcus. 2. Geographic variation among cyanobacteria: We completed 16S rRNA/ITS sequence and environmental chemistry data acquisition and are now analyzing results. 3. Microbial diversity in acid areas: Clone libraries were prepared and are being analyzed to study 16S rRNA-based diversity. More microsensor
fieldwork on sulfate reduction was conducted. Our results continue to demonstrate the amazing diversity of highly adapted microbial populations inhabiting geothermal resources that, like plant and animal species, have evolved due to ecological and geographic isolation. This reality of the microbial world must be dealt with in order to understand how microbial communities work. On the other hand, the same diversity represents an enormous resource of biotechnological potential. One implication of our geographic studies is that Yellowstone will likely need to consider management policies that minimize spring to spring contamination. Bioremediation Ecology--4. Studies of competitive fitness of phenanthrene-degrading isolates are continuing. 5. Mixture complexity effects on microbial community composition--manuscript submitted on sequential metabolism of n- and br-alkanes being due to population selection. Study of mixtures containing aromatic compounds completed; manuscript in
preparation. Manuscript on surfactant effects on population selection published. 6. Studies on the effect of natural organic matter/contaminant mixture interactions on microbial community complexity continue. Overall our results continue to demonstrate that a similar diversity of adapted microbial populations must be understood in order to predict how to use microorganisms in bioremediation of contaminants.
Impacts
Our findings on geothermal resources have and will continue to acquaint microbiologists with the enormous diversity of highly adapted microorganisms in natural systems and their biotechnological potential. It may be necessary to mange to prevent spring to spring cross-contamination in Yellowstone Park. Our findings on bioremediation ecology have and will continue to demonstrate the degree to which this diversity of highly adapted microorganisms must be understood in order to manage microbial bioremediation efforts.
Publications
- Grosser, R.J., Friedrich, M., Ward, D.M., and Inskeep, W.P. 2000. Effect of model sorptive phases on phenanthrene bioavailability: Different enrichment conditions influence bioavailability and selection of phenanthrene-degrading isolates. Appl. Environ. Microbiol. 66:2695-2702.
- Ramsing, N.B., Ferris, M.J., and Ward, D.M. 2000. Highly ordered vertical structure of Synechococcus populations within the one-millimeter thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66:1038-1049.
- Colores, G.M., Macur, R.E., Ward, D.M., and Inskeep, W.P. 2000. Microbial population shifts in soil as a function of surfactant application. Appl. Environ. Microbiol. 66:2959-2964.
- Friedrich, M., Grosser, R.J., Kern, E.A., Inskeep, W.P., and Ward, D.M. 2000. Effect of model sorptive phases on phenanthrene bioavailability: Molecular analysis of enrichments and isolates suggests selection based on bioavailability. Appl. Environ. Microbiol. 66:2703-2710.
|
|