publication . Article . 2017

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.

Hamilton, Joshua J.; Garcia, Sarahi L.; Brown, Brittany S.; Oyserman, Ben O.; Moya-Flores, Francisco; Bertilsson, Stefan; Malmstrom, Rex R.; Forest, Katrina T.; McMahon, Katherine D.;
Open Access
  • Published: 01 Aug 2017 Journal: volume 2, issue 4issn: 2379-5077, eissn: 2379-5077, Copyright policy
  • Publisher: eScholarship, University of California
Abstract
ABSTRACT An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U...
Subjects
free text keywords: systems biology, Biotechnology, Research Article, freshwater microbial ecology, Infectious Diseases, physiology, Microbiology, QR1-502, Editor's Pick, Biological Sciences, Bioengineering, Novel Systems Biology Techniques, Genetics, metatranscriptomics, metagenomics, Human Genome, metabolism, Biologiska vetenskaper
Funded by
NSF| Collaborative Research: MO: Forces Driving Microbial Community Diversity and Composition in Humic Lakes
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0702395
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| INSPIRE Track 1: Microbial systems biology in freshwater lakes: a new framework for scaling from genes to ecosystems
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1344254
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| LTER: Comparative Study of a Suite of Lakes in Wisconsin
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1440297
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
41 references, page 1 of 3

1. Borenstein E, Kupiec M, Feldman MW, Ruppin E. 2008. Large-scale reconstruction [OpenAIRE]

2. Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth's 4. Sangwan N, Xia F, Gilbert JA. 2016. Recovering complete and draft population

7. Orth JD, Thiele I, Palsson BØ. 2010. What is flux balance analysis? Nature

8. Arkin AP, Stevens RL, Cottingham RW, Maslov S, Henry CS, Dehal P, Ware D,

11. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK. 2002. Typical

12. Newton RJ, Kent AD, Triplett EW, McMahon KD. 2006. Microbial community

13. Wu QL, Zwart G, Schauer M, Kamst-Van Agterveld MP, Hahn MW. 2006.

14. Newton RJ, Jones SE, Helmus MR, McMahon KD. 2007. Phylogenetic ecology of

15. Wu X, Xi W, Ye W, Yang H. 2007. Bacterial community composition of a shallow

16. De Wever A, Van Der Gucht K, Muylaert K, Cousin S, Vyverman W. 2008. Clone

17. Humbert JF, Dorigo U, Cecchi P, Le Berre B, Debroas D, Bouvy M. 2009.

18. Ghai R, McMahon KD, Rodriguez-Valera F. 2012. Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environmental Microbiology Reports 4:29-35.

19. Buck U, Grossart H-P, Amann RI, Pernthaler J. 2009. Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environmental Microbiology 11:1854-1865. [OpenAIRE]

20. Salcher MM, Pernthaler J, Posch T. 2010. Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. Limnology and Oceanography 55:846-856. [OpenAIRE]

21. Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. 2012. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. The ISME Journal 6:113-123.

41 references, page 1 of 3
Abstract
ABSTRACT An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U...
Subjects
free text keywords: systems biology, Biotechnology, Research Article, freshwater microbial ecology, Infectious Diseases, physiology, Microbiology, QR1-502, Editor's Pick, Biological Sciences, Bioengineering, Novel Systems Biology Techniques, Genetics, metatranscriptomics, metagenomics, Human Genome, metabolism, Biologiska vetenskaper
Funded by
NSF| Collaborative Research: MO: Forces Driving Microbial Community Diversity and Composition in Humic Lakes
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0702395
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| INSPIRE Track 1: Microbial systems biology in freshwater lakes: a new framework for scaling from genes to ecosystems
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1344254
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| LTER: Comparative Study of a Suite of Lakes in Wisconsin
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1440297
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
41 references, page 1 of 3

1. Borenstein E, Kupiec M, Feldman MW, Ruppin E. 2008. Large-scale reconstruction [OpenAIRE]

2. Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth's 4. Sangwan N, Xia F, Gilbert JA. 2016. Recovering complete and draft population

7. Orth JD, Thiele I, Palsson BØ. 2010. What is flux balance analysis? Nature

8. Arkin AP, Stevens RL, Cottingham RW, Maslov S, Henry CS, Dehal P, Ware D,

11. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK. 2002. Typical

12. Newton RJ, Kent AD, Triplett EW, McMahon KD. 2006. Microbial community

13. Wu QL, Zwart G, Schauer M, Kamst-Van Agterveld MP, Hahn MW. 2006.

14. Newton RJ, Jones SE, Helmus MR, McMahon KD. 2007. Phylogenetic ecology of

15. Wu X, Xi W, Ye W, Yang H. 2007. Bacterial community composition of a shallow

16. De Wever A, Van Der Gucht K, Muylaert K, Cousin S, Vyverman W. 2008. Clone

17. Humbert JF, Dorigo U, Cecchi P, Le Berre B, Debroas D, Bouvy M. 2009.

18. Ghai R, McMahon KD, Rodriguez-Valera F. 2012. Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environmental Microbiology Reports 4:29-35.

19. Buck U, Grossart H-P, Amann RI, Pernthaler J. 2009. Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environmental Microbiology 11:1854-1865. [OpenAIRE]

20. Salcher MM, Pernthaler J, Posch T. 2010. Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. Limnology and Oceanography 55:846-856. [OpenAIRE]

21. Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. 2012. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. The ISME Journal 6:113-123.

41 references, page 1 of 3
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publication . Article . 2017

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.

Hamilton, Joshua J.; Garcia, Sarahi L.; Brown, Brittany S.; Oyserman, Ben O.; Moya-Flores, Francisco; Bertilsson, Stefan; Malmstrom, Rex R.; Forest, Katrina T.; McMahon, Katherine D.;