Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina

Carney, Laura T.; Wilkenfeld, Joshua S.; Lane, Pam D.; Solberg, Owen D.; Fuqua, Zachary B.; Cornelius, Nina G.; Gillespie, Shaunette; Williams, Kelly P.; Samocha, Tzachi M.; Lane, Todd W.

doi:10.1016/j.algal.2016.05.011

Title: Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina

Journal Article · Thu Jun 02 00:00:00 EDT 2016 · Algal Research

DOI:https://doi.org/10.1016/j.algal.2016.05.011· OSTI ID:1271304

Carney, Laura T. ^[1]; Wilkenfeld, Joshua S. ^[2]; Lane, Pam D. ^[1]; Solberg, Owen D. ^[1]; Fuqua, Zachary B. ^[2]; Cornelius, Nina G. ^[2]; Gillespie, Shaunette ^[2]; Williams, Kelly P. ^[1];

^[2]; Lane, Todd W. ^[1]

Sandia National Lab. (SNL-CA), Livermore, CA (United States). Systems Biology
Texas A&M AgriLife Research and Extension Center, Corpus Christi, TX (United States). AgriLife Research Mariculture Lab. at Flour Bluff

Productivity of algal mass culture can be severely reduced by contaminating organisms. It is, therefore, important to identify contaminants, determine their effect on productivity and, ultimately, develop countermeasures against such contamination. In this paper, we utilized microbiome analysis by second-generation sequencing of small subunit rRNA genes to characterize the predator and pathogen burden of open raceway cultures of Nannochloropsis salina. Samples were analyzed from replicate raceways before and after crashes. In one culture cycle, we identified two algivorous species, the rotifer Brachionus and gastrotrich Chaetonotus, the presence of which may have contributed to the loss of algal biomass. In the second culture cycle, the raceways were treated with hypochlorite in an unsuccessful attempt to interdict the crash. Finally, our analyses were shown to be an effective strategy for the identification of the biological contaminants and the characterization of intervention strategies.

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Research Organization:: Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO)

Contributing Organization:: Texas A&M AgriLife Research and Extension Center, Corpus Christi, TX (United States)

Grant/Contract Number:: AC04-94AL85000; NL0022897

OSTI ID:: 1271304

Alternate ID(s):: OSTI ID: 1323980

Report Number(s):: SAND2015-5591J; PII: S2211926416301679

Journal Information:: Algal Research, Vol. 17; ISSN 2211-9264

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 42 works

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References (29)

Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the compositae Baldwin, Bruce G. Molecular Phylogenetics and Evolution, Vol. 1, Issue 1 https://doi.org/10.1016/1055-7903(92)90030-K	journal	March 1992
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads Bartram, Andrea K.; Lynch, Michael D. J.; Stearns, Jennifer C. Applied and Environmental Microbiology, Vol. 77, Issue 11 https://doi.org/10.1128/AEM.02772-10	journal	April 2011
Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill Bik, Holly M.; Halanych, Kenneth M.; Sharma, Jyotsna PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0038550	journal	June 2012
Microbiome analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor Carney, Laura T.; Reinsch, Sigrid S.; Lane, Pamela D. Algal Research, Vol. 4 https://doi.org/10.1016/j.algal.2013.11.006	journal	April 2014
Biodiesel from microalgae Chisti, Yusuf Biotechnology Advances, Vol. 25, Issue 3, p. 294-306 https://doi.org/10.1016/j.biotechadv.2007.02.001	journal	May 2007
Interactions Between Bacteria and Algae in Aquatic Ecosystems Cole, J. J. Annual Review of Ecology and Systematics, Vol. 13, Issue 1 https://doi.org/10.1146/annurev.es.13.110182.001451	journal	November 1982
Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity Dunthorn, Micah; Klier, Julia; Bunge, John Journal of Eukaryotic Microbiology, Vol. 59, Issue 2 https://doi.org/10.1111/j.1550-7408.2011.00602.x	journal	January 2012
Phlyctidium scenedesmi spec. nova, a new chytrid destroying mass cultures of algae Fott, Bohuslav Zeitschrift für allgemeine Mikrobiologie, Vol. 7, Issue 2 https://doi.org/10.1002/jobm.19670070203	journal	January 1967
Intersite epibiosis characterization on dominant mangrove crustacean species from Malaysia Fernandez-Leborans, Gregorio; Hanamura, Yukio; Siow, Ryon Contributions to Zoology, Vol. 78, Issue 1 https://doi.org/10.1163/18759866-07801002	journal	April 2009
Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited Hess, Sebastian; Sausen, Nicole; Melkonian, Michael PLoS ONE, Vol. 7, Issue 2 https://doi.org/10.1371/journal.pone.0031165	journal	February 2012
Fundamental Studies on Physiology of Rotifer for its Mass Culture-I [大量培養の基礎としてのシオミズツボワムシの生理学的研究-I.] Hirayama, Kazutsugu; Ogawa, Shichiro NIPPON SUISAN GAKKAISHI, Vol. 38, Issue 11 https://doi.org/10.2331/suisan.38.1207	journal	January 1972
Isolation and characterization of a novel chytrid species (phylum Blastocladiomycota), parasitic on the green alga Haematococcus Hoffman, Yoram; Aflalo, Claude; Zarka, Aliza Mycological Research, Vol. 112, Issue 1 https://doi.org/10.1016/j.mycres.2007.09.002	journal	January 2008
Selectivity of the rotifer Brachionus plicatilis fed mixtures of algal species with various cell volumes and cell densities: Feed selectivity of rotifers Hotos, G. N. Aquaculture Research, Vol. 33, Issue 12 https://doi.org/10.1046/j.1365-2109.2002.00746.x	journal	September 2002
Algicidal Marine Bacteria Isolated from Northern Hiroshima Bay, Japan Imai, Ichiro; Ishida, Yuzaburo; Sakaguchi, Keiichi Fisheries science, Vol. 61, Issue 4 https://doi.org/10.2331/fishsci.61.628	journal	January 1995
Bacterial Diversity Associated with the Rotifer Brachionus plicatilis sp. Complex Determined by Culture-Dependent and -Independent Methods Ishino, Ryota; Iehata, Shunpei; Nakano, Miyo Biocontrol Science, Vol. 17, Issue 1 https://doi.org/10.4265/bio.17.51	journal	January 2012
Epizooic ciliates (Vorticella sp.) compete for food with their host Daphnia longispina in a small polyhumic lake Kankaala, P.; Eloranta, P. Oecologia, Vol. 73, Issue 2 https://doi.org/10.1007/BF00377508	journal	January 1987
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Metagenome of microorganisms associated with the toxic Cyanobacteria Microcystis aeruginosa analyzed using the 454 sequencing platform Li, Nan; Zhang, Lei; Li, Fuchao Chinese Journal of Oceanology and Limnology, Vol. 29, Issue 3 https://doi.org/10.1007/s00343-011-0056-0	journal	May 2011
FLASH: fast length adjustment of short reads to improve genome assemblies Magoc, T.; Salzberg, S. L. Bioinformatics, Vol. 27, Issue 21 https://doi.org/10.1093/bioinformatics/btr507	journal	September 2011
Algicidal Bacteria in the Sea and their Impact on Algal Blooms1 Mayali, Xavier; Azam, Farooq The Journal of Eukaryotic Microbiology, Vol. 51, Issue 2 https://doi.org/10.1111/j.1550-7408.2004.tb00538.x	journal	March 2004
Contamination Management in Low Cost Open Algae Ponds for Biofuels Production McBride, Robert C.; Lopez, Salvador; Meenach, Chris Industrial Biotechnology, Vol. 10, Issue 3 https://doi.org/10.1089/ind.2013.0036	journal	June 2014
Analysis of bacterial communities in Nannochloropsis sp. cultures used for larval fish production Nakase, Gentoku; Eguchi, Mitsuru Fisheries Science, Vol. 73, Issue 3 https://doi.org/10.1111/j.1444-2906.2007.01366.x	journal	June 2007
Wastewater treatment high rate algal ponds for biofuel production Park, J. B. K.; Craggs, R. J.; Shilton, A. N. Bioresource Technology, Vol. 102, Issue 1, p. 35-42 https://doi.org/10.1016/j.biortech.2010.06.158	journal	January 2011
Ecology of the marine protists, the Labyrinthulomycetes (Thraustochytrids and Labyrinthulids) Raghukumar, Seshagiri European Journal of Protistology, Vol. 38, Issue 2 https://doi.org/10.1078/0932-4739-00832	journal	January 2002
A financial assessment of two alternative cultivation systems and their contributions to algae biofuel economic viability Richardson, James W.; Johnson, Myriah D.; Zhang, Xuezhi Algal Research, Vol. 4 https://doi.org/10.1016/j.algal.2013.12.003	journal	April 2014
Effects of Bacterial Coexistence on the Growth of a Marine Diatom Chaetoceros gracilis Fisheries science, Vol. 62, Issue 1, p. 40-43 https://doi.org/10.2331/fishsci.62.40	journal	January 1996
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna Tang, C. Q.; Leasi, F.; Obertegger, U. Proceedings of the National Academy of Sciences, Vol. 109, Issue 40 https://doi.org/10.1073/pnas.1209160109	journal	September 2012
Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture Thomas, Vincent; Casson, Nicola; Greub, Gilbert Environmental Microbiology, Vol. 8, Issue 12 https://doi.org/10.1111/j.1462-2920.2006.01094.x	journal	December 2006
Population growth dynamics of the rotifer Brachionus plicatilis cultured in non-limiting food condition Y�fera, M.; Navarro, N. Hydrobiologia, Vol. 313-314, Issue 1 https://doi.org/10.1007/BF00025977	journal	November 1995

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Non-photochemical quenching, a non-invasive probe for monitoring microalgal grazing: influence of grazing-mediated total ammonia-nitrogen Deore, Pranali; Beardall, John; Noronha, Santosh Taylor & Francis https://doi.org/10.6084/m9.figshare.11985318.v1	text	January 2020
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Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes Reese, Kristen L.; Fisher, Carolyn L.; Lane, Pamela D. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-50125-z	journal	September 2019
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Non-photochemical quenching, a non-invasive probe for monitoring microalgal grazing: an early indicator of predation by Oxyrrhis marina and Euplotes sp. Deore, Pranali; Karthikaichamy, Anbarasu; Beardall, John Taylor & Francis https://doi.org/10.6084/m9.figshare.11972988	text	January 2020

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Title: Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina

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Cited By (7)

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