Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures
Abstract
Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalentmore »
- Authors:
-
- Sandia National Lab. (SNL-CA), Livermore, CA (United States)
- Sandia National Lab. (SNL-CA), Livermore, CA (United States); Univ. of the Philippines, Diliman Quezon City (Philippines)
- Publication Date:
- Research Org.:
- Sandia National Lab. (SNL-CA), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1343273
- Report Number(s):
- SAND-2016-1584J
Journal ID: ISSN 0095-3628; PII: 746
- Grant/Contract Number:
- AC04-94AL85000
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Microbial Ecology
- Additional Journal Information:
- Journal Volume: 72; Journal Issue: 1; Journal ID: ISSN 0095-3628
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; biosystem; microbiota; algae; stability
Citation Formats
Geng, Haifeng, Sale, Kenneth L., Tran-Gyamfi, Mary Bao, Lane, Todd W., and Yu, Eizadora T. Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures. United States: N. p., 2016.
Web. doi:10.1007/s00248-016-0746-4.
Geng, Haifeng, Sale, Kenneth L., Tran-Gyamfi, Mary Bao, Lane, Todd W., & Yu, Eizadora T. Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures. United States. https://doi.org/10.1007/s00248-016-0746-4
Geng, Haifeng, Sale, Kenneth L., Tran-Gyamfi, Mary Bao, Lane, Todd W., and Yu, Eizadora T. 2016.
"Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures". United States. https://doi.org/10.1007/s00248-016-0746-4. https://www.osti.gov/servlets/purl/1343273.
@article{osti_1343273,
title = {Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures},
author = {Geng, Haifeng and Sale, Kenneth L. and Tran-Gyamfi, Mary Bao and Lane, Todd W. and Yu, Eizadora T.},
abstractNote = {Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.},
doi = {10.1007/s00248-016-0746-4},
url = {https://www.osti.gov/biblio/1343273},
journal = {Microbial Ecology},
issn = {0095-3628},
number = 1,
volume = 72,
place = {United States},
year = {Tue Mar 08 00:00:00 EST 2016},
month = {Tue Mar 08 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes
journal, October 2010
- Edwards, Jennifer L.; Smith, Darren L.; Connolly, John
- Genes, Vol. 1, Issue 3
Unlocking Short Read Sequencing for Metagenomics
journal, July 2010
- Rodrigue, Sébastien; Materna, Arne C.; Timberlake, Sonia C.
- PLoS ONE, Vol. 5, Issue 7
Growth interactions between marine dinoflagellates in multispecies culture experiments
journal, January 1979
- Kayser, H.
- Marine Biology, Vol. 52, Issue 4
Biodiesel from algae: challenges and prospects
journal, June 2010
- Scott, Stuart A.; Davey, Matthew P.; Dennis, John S.
- Current Opinion in Biotechnology, Vol. 21, Issue 3
Microbiome analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor
journal, April 2014
- Carney, Laura T.; Reinsch, Sigrid S.; Lane, Pamela D.
- Algal Research, Vol. 4
Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism
journal, September 2009
- Amin, S. A.; Green, D. H.; Hart, M. C.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 40
The contribution of species richness and composition to bacterial services
journal, August 2005
- Bell, Thomas; Newman, Jonathan A.; Silverman, Bernard W.
- Nature, Vol. 436, Issue 7054
Molecular eco-systems biology: towards an understanding of community function
journal, June 2008
- Raes, Jeroen; Bork, Peer
- Nature Reviews Microbiology, Vol. 6, Issue 9
Parallel Processing of Substrate Correlates with Greater Functional Stability in Methanogenic Bioreactor Communities Perturbed by Glucose
journal, September 2000
- Hashsham, S. A.; Fernandez, A. S.; Dollhopf, S. L.
- Applied and Environmental Microbiology, Vol. 66, Issue 9
UniFrac: an effective distance metric for microbial community comparison
journal, September 2010
- Lozupone, Catherine; Lladser, Manuel E.; Knights, Dan
- The ISME Journal, Vol. 5, Issue 2
Involvement of an Extracellular Protease in Algicidal Activity of the Marine Bacterium Pseudoalteromonas sp. Strain A28
journal, October 2000
- Lee, S. -o.; Kato, J.; Takiguchi, N.
- Applied and Environmental Microbiology, Vol. 66, Issue 10
Exploiting diversity and synthetic biology for the production of algal biofuels
journal, August 2012
- Georgianna, D. Ryan; Mayfield, Stephen P.
- Nature, Vol. 488, Issue 7411
Interactions of the Algicidal Bacterium Kordia algicida with Diatoms: Regulated Protease Excretion for Specific Algal Lysis
journal, June 2011
- Paul, Carsten; Pohnert, Georg
- PLoS ONE, Vol. 6, Issue 6
Determination of Orthophosphate in Aqueous Solutions Containing Labile Organic and Inorganic Phosphorus Compounds1
journal, January 1977
- Dick, W. A.; Tabatabai, M. A.
- Journal of Environment Quality, Vol. 6, Issue 1
Environmental Biology of the Marine Roseobacter Lineage
journal, October 2006
- Wagner-Döbler, Irene; Biebl, Hanno
- Annual Review of Microbiology, Vol. 60, Issue 1
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean: Genomic content of uncultivated marine Bacteroidetes
journal, September 2011
- Gómez-Pereira, Paola R.; Schüler, Margarete; Fuchs, Bernhard M.
- Environmental Microbiology, Vol. 14, Issue 1
Molecular mechanisms underlying roseobacter–phytoplankton symbioses
journal, June 2010
- Geng, Haifeng; Belas, Robert
- Current Opinion in Biotechnology, Vol. 21, Issue 3
Annually reoccurring bacterial communities are predictable from ocean conditions
journal, August 2006
- Fuhrman, J. A.; Hewson, I.; Schwalbach, M. S.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 35
Determination of nitrate in sea water by cadmium-copper reduction to nitrite
journal, February 1967
- Wood, E. D.; Armstrong, F. A. J.; Richards, F. A.
- Journal of the Marine Biological Association of the United Kingdom, Vol. 47, Issue 1
A Broad Spectrum Artificial sea Water Medium for Coastal and open Ocean Phytoplankton1
journal, March 1980
- Harrison, Paul J.; Waters, Rosemary E.; Taylor, F. J. R.
- Journal of Phycology, Vol. 16, Issue 1
Bacterial community transcription patterns during a marine phytoplankton bloom: Phytoplankton bloom metatranscriptome
journal, October 2011
- Rinta-Kanto, Johanna M.; Sun, Shulei; Sharma, Shalabh
- Environmental Microbiology, Vol. 14, Issue 1
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
journal, August 2010
- McCarren, J.; Becker, J. W.; Repeta, D. J.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 38
FragGeneScan: predicting genes in short and error-prone reads
journal, August 2010
- Rho, Mina; Tang, Haixu; Ye, Yuzhen
- Nucleic Acids Research, Vol. 38, Issue 20
Eukaryotic and prokaryotic microbial communities during microalgal biomass production
journal, November 2012
- Lakaniemi, Aino-Maija; Hulatt, Chris J.; Wakeman, Kathryn D.
- Bioresource Technology, Vol. 124
Bacterial community associated with Pfiesteria-like dinoflagellate cultures
journal, June 2001
- Alavi, Mohammad; Miller, Todd; Erlandson, Karn
- Environmental Microbiology, Vol. 3, Issue 6
Metagenome Survey of a Multispecies and Alga-Associated Biofilm Revealed Key Elements of Bacterial-Algal Interactions in Photobioreactors
journal, August 2013
- Krohn-Molt, Ines; Wemheuer, Bernd; Alawi, Malik
- Applied and Environmental Microbiology, Vol. 79, Issue 20
Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom
journal, May 2012
- Teeling, H.; Fuchs, B. M.; Becher, D.
- Science, Vol. 336, Issue 6081
Bacterial community structures are unique and resilient in full-scale bioenergy systems
journal, February 2011
- Werner, J. J.; Knights, D.; Garcia, M. L.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
Marine diatom species harbour distinct bacterial communities: Marine diatom species harbour distinct bacterial communities
journal, March 2005
- Grossart, Hans-Peter; Levold, Florian; Allgaier, Martin
- Environmental Microbiology, Vol. 7, Issue 6
Algicidal Bacteria in the Sea and their Impact on Algal Blooms1
journal, March 2004
- Mayali, Xavier; Azam, Farooq
- The Journal of Eukaryotic Microbiology, Vol. 51, Issue 2
Meta-IDBA: a de Novo assembler for metagenomic data
journal, June 2011
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 27, Issue 13
Microbial Population Structures in the Deep Marine Biosphere
journal, October 2007
- Huber, J. A.; Mark Welch, D. B.; Morrison, H. G.
- Science, Vol. 318, Issue 5847
The Long-Term Stability of the Human Gut Microbiota
journal, July 2013
- Faith, Jeremiah J.; Guruge, Janaki L.; Charbonneau, Mark
- Science, Vol. 341, Issue 6141
Reductions in grassland species evenness increase dicot seedling invasion and spittle bug infestation
journal, September 2002
- Wilsey, Brian J.; Polley, H. Wayne
- Ecology Letters, Vol. 5, Issue 5
Microbial community structure and its functional implications
journal, May 2009
- Fuhrman, Jed A.
- Nature, Vol. 459, Issue 7244
Marine microbial diversity: can it be determined?
journal, June 2006
- Pedrós-Alió, Carlos
- Trends in Microbiology, Vol. 14, Issue 6
Production of the Antimicrobial Secondary Metabolite Indigoidine Contributes to Competitive Surface Colonization by the Marine Roseobacter Phaeobacter sp. Strain Y4I
journal, May 2012
- Cude, W. Nathan; Mooney, Jason; Tavanaei, Arash A.
- Applied and Environmental Microbiology, Vol. 78, Issue 14
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
journal, December 2005
- Lozupone, C.; Knight, R.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
Algae acquire vitamin B12 through a symbiotic relationship with bacteria
journal, November 2005
- Croft, Martin T.; Lawrence, Andrew D.; Raux-Deery, Evelyne
- Nature, Vol. 438, Issue 7064
Synthetic ecology – A way forward for sustainable algal biofuel production?
journal, November 2012
- Kazamia, Elena; Aldridge, David C.; Smith, Alison G.
- Journal of Biotechnology, Vol. 162, Issue 1
Initial community evenness favours functionality under selective stress
journal, March 2009
- Wittebolle, Lieven; Marzorati, Massimo; Clement, Lieven
- Nature, Vol. 458, Issue 7238
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
journal, April 2011
- Bartram, Andrea K.; Lynch, Michael D. J.; Stearns, Jennifer C.
- Applied and Environmental Microbiology, Vol. 77, Issue 11
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Algicidal Effects of a Novel MarinePseudoalteromonas Isolate (Class Proteobacteria, Gamma Subdivision) on Harmful Algal Bloom Species of the GeneraChattonella, Gymnodinium, andHeterosigma
journal, August 1998
- Lovejoy, Connie; Bowman, John P.; Hallegraeff, Gustaaf M.
- Applied and Environmental Microbiology, Vol. 64, Issue 8
Works referencing / citing this record:
Analysis of microbiota in cultures of the green microalga Tetraselmis suecica
journal, April 2019
- Piampiano, Elisa; Pini, Francesco; Biondi, Natascia
- European Journal of Phycology, Vol. 54, Issue 3
Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds
journal, July 2016
- Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.
- Frontiers in Microbiology, Vol. 7