in

Tracing the path of carbon export in the ocean though DNA sequencing of individual sinking particles

  • Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237.

    CAS 
    Article 

    Google Scholar 

  • Volk T, Hoffert M. Ocean carbon pumps: analysis of relative strengths and efficiencies in ocean-driven atmospheric CO2 changes. Geophys Monogr Ser. 1985;32:99–110.

    Google Scholar 

  • Boyd PW, Claustre H, Levy M, Siegel DA, Weber T. Multi-faceted particle pumps drive carbon sequestration in the ocean. Nature. 2019;568:327–35.

    CAS 
    Article 

    Google Scholar 

  • Siegel DA, Buesseler KO, Doney SC, Sailley SF, Behrenfeld MJ, Boyd PW. Global assessment of ocean carbon export by combining satellite observations and food-web models. Glob Biogeochem Cycles. 2014;28:181–196.

  • Henson SA, Sanders R, Madsen E, Morris PJ, Le Moigne F, Quartly GD. A reduced estimate of the strength of the ocean’s biological carbon pump. Geophys Res Lett. 2011;38:L04606.

    Article 

    Google Scholar 

  • Boyd PW, Trull TW. Understanding the export of biogenic particles in oceanic waters: is there consensus? Prog Oceanogr. 2007;72:276–312.

    Article 

    Google Scholar 

  • Werdell PJ, Behrenfeld MJ, Bontempi PS, Boss E, Cairns B, Davis GT, et al. The plankton, aerosol, cloud, ocean ecosystem mission: status, science, advances. Bull Am Meteorol Soc. 2019;100:1775–94.

    Article 

    Google Scholar 

  • Picheral M, Guidi L, Stemmann L, Karl DM, Iddaoud G, Gorsky G. The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnol Oceanogr-Methods. 2010;8:462–73.

    Article 

    Google Scholar 

  • Olson RJ, Sosik HM. A submersible imaging-in-flow instrument to analyze nano-and microplankton: imaging FlowCytobot. Limnol Oceanogr Methods. 2007;5:195–203.

    Article 

    Google Scholar 

  • de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.

  • Scholin C, Birch J, Jensen S, Marin R III, Massion E, Pargett D, et al. The quest to develop ecogenomic sensors: a 25-year history of the Environmental Sample Processor (ESP) as a case study. Oceanography. 2017;30:100–13.

    Article 

    Google Scholar 

  • Cruz BN, Brozak S, Neuer S. Microscopy and DNA-based characterization of sinking particles at the Bermuda Atlantic Time-series Study station point to zooplankton mediation of particle flux. Limnol Oceanogr. 2021;66:3697–713.

    CAS 
    Article 

    Google Scholar 

  • Amacher J, Neuer S, Lomas M. DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study. Deep Sea Res Part II Top Stud Oceanogr. 2013;93:71–83.

    CAS 
    Article 

    Google Scholar 

  • Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol. 2015;6:469.

    Article 

    Google Scholar 

  • Preston CM, Durkin CA, Yamahara KM DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean. Deep Sea Res Part II Top Stud Oceanogr. 2019;173:104708.

  • Gutierrez-Rodriguez A, Stukel MR, Lopes dos Santos A, Biard T, Scharek R, Vaulot D, et al. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. ISME J. 2019;13:964–76.

    CAS 
    Article 

    Google Scholar 

  • Boeuf D, Edwards BR, Eppley JM, Hu SK, Poff KE, Romano AE, et al. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci. 2019;116:11824.

    CAS 
    Article 

    Google Scholar 

  • Silver MW, Gowing MM. The “particle” flux: Origins and biological components. Prog Oceanogr. 1991;26:75–113.

    Article 

    Google Scholar 

  • Ebersbach F, Assmy P, Martin P, Schulz I, Wolzenburg S, Nöthig E-M. Particle flux characterisation and sedimentation patterns of protistan plankton during the iron fertilisation experiment LOHAFEX in the Southern Ocean. Deep Sea Res Part Oceanogr Res Pap. 2014;89:94–103.

    CAS 
    Article 

    Google Scholar 

  • Waite A, Bienfang PK, Harrison PJ. Spring bloom sedimentation in a subarctic ecosystem. II. Succession and sedimentation. Mar Biol. 1992;114:131–8.

    Article 

    Google Scholar 

  • Venrick E, Lange C, Reid F, Dever EP. Temporal patterns of species composition of siliceous phytoplankton flux in the Santa Barbara Basin. J Plankton Res. 2007;30:283–97.

    Article 

    Google Scholar 

  • Waite AM, Safi KA, Hall JA, Nodder SD. Mass sedimentation of picoplankton embedded in organic aggregates. Limnol Oceanogr. 2000;45:87–97.

    Article 

    Google Scholar 

  • Valencia B, Stukel MR, Allen AE, McCrow JP, Rabines A, Palenik B, et al. Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export. Environ Microbiol. 2021;23:6743–8.

    Article 

    Google Scholar 

  • Scharek R, Tupas LM, Karl DM. Diatom fluxes to the deep sea in the oligotrophic North Pacific gyre at Station ALOHA. Mar Ecol Prog Ser. 1999;182:55–67.

    Article 

    Google Scholar 

  • Beaulieu S. Accumulation and fate of phytodetritus on the sea floor. Oceanogr Mar Biol Annu Rev. 2002;40:171–232.

    Google Scholar 

  • Ikenoue T, Kimoto K, Okazaki Y, Sato M, Honda MC, Takahashi K, et al. Phaeodaria: an important carrier of particulate organic carbon in the mesopelagic twilight zone of the North Pacific Ocean. Glob Biogeochem Cycles. 2019;33:1146–60.

    CAS 
    Article 

    Google Scholar 

  • Smith KL, Ruhl HA, Huffard CL, Messié M, Kahru M. Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific. Proc Natl Acad Sci. 2018;115:12235.

    CAS 
    Article 

    Google Scholar 

  • Durkin CA, Buesseler KO, Cetinić I, Estapa ML, Kelly RP, Omand M. A visual tour of carbon export by sinking particles. Glob Biogeochem Cycles. 2021;35:e2021GB006985.

    CAS 
    Article 

    Google Scholar 

  • Estapa ML, Valdes J, Tradd K, Sugar J, Omand M, Buesseler K. The neutrally buoyant sediment trap: two decades of progress. J Atmospheric Ocean Technol. 2020;37:957–973.

  • Rainville L, Pinkel R. Wirewalker: An autonomous wave-powered vertical profiler. J Atmos Ocean Technol. 2001;18:1048–51.

    Article 

    Google Scholar 

  • Durkin CA, Estapa ML, Buesseler KO. Observations of carbon export by small sinking particles in the upper mesopelagic. Mar Chem. 2015;175:72–81.

    CAS 
    Article 

    Google Scholar 

  • Malmstrom R RNAlater Recipe. protocols.io. https://doi.org/10.17504/protocols.io.c56y9d. Accessed 2 Oct 2018.

  • Mackey MD, Mackey DJ, Higgins HW, Wright SW. CHEMTAX—a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton. Mar Ecol Prog Ser. 1996;144:265–83.

    CAS 
    Article 

    Google Scholar 

  • Massana R, Murray AE, Preston CM, DeLong EF. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol. 1997;63:50.

    CAS 
    Article 

    Google Scholar 

  • Stoeck T, Bass D, Nebel M, Christen R, Jones M, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.

    CAS 
    Article 

    Google Scholar 

  • Penna A, Casabianca S, Guerra A, Vernesi C, Scardi M. Analysis of phytoplankton assemblage structure in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences. Mar Genomics. 2017;36:49–55.

  • Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.

    CAS 
    Article 

    Google Scholar 

  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.

    CAS 
    Article 

    Google Scholar 

  • Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2012;41:D597–D604.

    Article 

    Google Scholar 

  • Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6:90.

    Article 

    Google Scholar 

  • Tomas CR. Identifying marine phytoplankton. Elsevier; 1997.

  • Hasle GR, Syvertsen EE. Marine diatoms. In: Tomas CR (ed). Identifying marine phytoplankton. San Diego, CA, USA: Academic Press; 1997. pp 5–385.

  • Godhe A, Asplund ME, Härnström K, Saravanan V, Tyagi A, Karunasagar I. Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl Environ Microbiol. 2008;74:7174–82.

    CAS 
    Article 

    Google Scholar 

  • Smayda TJ. The suspension and sinking of phytoplankton in the sea. Oceanogr Mar Biol Annu Rev. 1970;8:353–414.

    Google Scholar 

  • Sancetta C, Villareal T, Falkowski P. Massive fluxes of rhizosolenid diatoms: a common occurrence? Limnol Oceanogr. 1991;36:1452–7.

    Article 

    Google Scholar 

  • Goldman JC. Potential role of large oceanic diatoms in new primary production. Deep Sea Res Part Oceanogr Res Pap. 1993;40:159–68.

    Article 

    Google Scholar 

  • Kemp AE, Pike J, Pearce RB, Lange CB. The “Fall dump”—a new perspective on the role of a “shade flora” in the annual cycle of diatom production and export flux. Deep Sea Res Part II Top Stud Oceanogr. 2000;47:2129–54.

    Article 

    Google Scholar 

  • Villareal TA, Woods S, Moore JK, CulverRymsza K. Vertical migration of Rhizosolenia mats and their significance to NO3− fluxes in the central North Pacific gyre. J Plankton Res. 1996;18:1103–21.

    Article 

    Google Scholar 

  • Smayda TJ. Normal and accelerated sinking of phytoplankton in the sea. Mar Geol. 1971;11:105–22.

    Article 

    Google Scholar 

  • Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada NA. DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLOS ONE. 2021;16:e0245936.

    CAS 
    Article 

    Google Scholar 

  • Omand MM, Govindarajan R, He J, Mahadevan A. Sinking flux of particulate organic matter in the oceans: sensitivity to particle characteristics. Sci Rep. 2020;10:5582.

    CAS 
    Article 

    Google Scholar 

  • DeVries T, Liang J-H, Deutsch C. A mechanistic particle flux model applied to the oceanic phosphorus cycle. Biogeosciences. 2014;11:5381–98.

    Article 

    Google Scholar 

  • Siegel DA, Buesseler KO, Behrenfeld MJ, Benitez-Nelson CR, Boss E, Brzezinski MA, et al. Prediction of the export and fate of global ocean net primary production: the EXPORTS science plan. Front Mar Sci. 2016;3:22.

    Article 

    Google Scholar 

  • NASA Ocean Biology Processing Group. MODIS-Aqua Level 3 mapped chlorophyll data version R2018.0. 2017. NASA Ocean Biology DAAC. https://doi.org/10.5067/AQUA/MODIS/L3M/CHL/2018.


  • Source: Ecology - nature.com

    Empowering people to adapt on the frontlines of climate change

    Amy Moran-Thomas receives the Edgerton Faculty Achievement Award