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Brunson JK, Thukral M, Ryan JP, Anderson CR, Kolody BC, James C, Chavez FP, Leaw CP, Rabines AJ, Venepally P, Zheng H, Kudela RM, Smith GJ, Moore BS, Allen AE. Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom. bioRxiv 2023:2023.11.02.565333. [PMID: 37961417 PMCID: PMC10635071 DOI: 10.1101/2023.11.02.565333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis , this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis ( dab ) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters ( sit1 ) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of the dabA and sit1 genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adapted Pseudo-nitzschia genus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxic Pseudo-nitzschia blooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms. Significance Pseudo-nitzschia diatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenic Pseudo-nitzschia species during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.
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Sandoval-Belmar M, Smith J, Moreno AR, Anderson C, Kudela RM, Sutula M, Kessouri F, Caron DA, Chavez FP, Bianchi D. A cross-regional examination of patterns and environmental drivers of Pseudo-nitzschia harmful algal blooms along the California coast. Harmful Algae 2023; 126:102435. [PMID: 37290883 DOI: 10.1016/j.hal.2023.102435] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/05/2023] [Accepted: 04/16/2023] [Indexed: 06/10/2023]
Abstract
Pseudo-nitzschia species with the ability to produce the neurotoxin domoic acid (DA) are the main cause of harmful algal blooms (HABs) along the U.S. West Coast, with major impacts on ecosystems, fisheries, and human health. While most Pseudo-nitzschia (PN) HAB studies to date have focused on their characteristics at specific sites, few cross-regional comparisons exist, and mechanistic understanding of large-scale HAB drivers remains incomplete. To close these gaps, we compiled a nearly 20-year time series of in situ particulate DA and environmental observations to characterize similarities and differences in PN HAB drivers along the California coast. We focus on three DA hotspots with the greatest data density: Monterey Bay, the Santa Barbara Channel, and the San Pedro Channel. Coastwise, DA outbreaks are strongly correlated with upwelling, chlorophyll-a, and silicic acid limitation relative to other nutrients. Clear differences also exist across the three regions, with contrasting responses to climate regimes across a north to south gradient. In Monterey Bay, PN HAB frequency and intensity increase under relatively nutrient-poor conditions during anomalously low upwelling intensities. In contrast, in the Santa Barbara and San Pedro Channels, PN HABs are favored under cold, nitrogen-rich conditions during more intense upwelling. These emerging patterns provide insights on ecological drivers of PN HABs that are consistent across regions and support the development of predictive capabilities for DA outbreaks along the California coast and beyond.
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Affiliation(s)
- Marco Sandoval-Belmar
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095-1565, United States of America.
| | - Jayme Smith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626-1437, United States of America
| | - Allison R Moreno
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095-1565, United States of America
| | - Clarissa Anderson
- Southern California Coastal Ocean Observing System, Scripps Institution of Oceanography, La Jolla, CA, United States of America
| | - Raphael M Kudela
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Martha Sutula
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626-1437, United States of America
| | - Fayçal Kessouri
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095-1565, United States of America; Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626-1437, United States of America
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, United States of America
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Daniele Bianchi
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095-1565, United States of America
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Messié M, Sherlock RE, Huffard CL, Pennington JT, Choy CA, Michisaki RP, Gomes K, Chavez FP, Robison BH, Smith KL. Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor. Proc Natl Acad Sci U S A 2023; 120:e2214567120. [PMID: 36947518 PMCID: PMC10068760 DOI: 10.1073/pnas.2214567120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/10/2023] [Indexed: 03/23/2023] Open
Abstract
Long-term biological time series that monitor ecosystems across the ocean's full water column are extremely rare. As a result, classic paradigms are yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multidecadal time series spanning surface (0 m), midwater (200 to 1,000 m), and benthic (~4,000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increase in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), which dictate how long upwelling-driven changes persist within each community.
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Affiliation(s)
- Monique Messié
- Monterey Bay Aquarium Research Institute, Moss Landing, CA95039
| | - Rob E. Sherlock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA95039
| | | | | | - C. Anela Choy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA95039
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA92093
| | | | - Kevin Gomes
- Monterey Bay Aquarium Research Institute, Moss Landing, CA95039
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Meyer R, Davies N, Pitz KJ, Meyer C, Samuel R, Anderson J, Appeltans W, Barker K, Chavez FP, Duffy JE, Goodwin KD, Hudson M, Hunter ME, Karstensen J, Laney CM, Leinen M, Mabee P, Macklin JA, Muller-Karger F, Pade N, Pearlman J, Phillips L, Provoost P, Santi I, Schigel D, Schriml LM, Soccodato A, Suominen S, Thibault KM, Ung V, van de Kamp J, Wallis E, Walls R, Buttigieg PL. The founding charter of the Omic Biodiversity Observation Network (Omic BON). Gigascience 2022; 12:giad068. [PMID: 37632753 PMCID: PMC10460158 DOI: 10.1093/gigascience/giad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023] Open
Abstract
Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.
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Affiliation(s)
- Raïssa Meyer
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Faculty of Geosciences, University of Bremen, Bremen 28359, Germany
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Neil Davies
- Gump South Pacific Research Station, University of California Berkeley, Moorea 98728, French Polynesia
- Berkeley Institute for Data Science, University of California, Berkeley, CA 94720, USA
| | - Kathleen J Pitz
- Science Department, Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Chris Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Robyn Samuel
- School of Ocean and Earth Science, University of Southampton, Southampton SO17 1BJ, UK
- Ocean Technology and Engineering Group, National Oceanography Center, Southampton SO14 3ZH, UK
| | - Jane Anderson
- Department of Anthropology, New York University, New York City, NY 10012, USA
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Katharine Barker
- Global Genome Biodiversity Network Secretariat Office, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Francisco P Chavez
- Science Department, Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network and MarineGEO Program, Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
| | - Kelly D Goodwin
- National Oceanic & Atmospheric Administration, NOAA Ocean Exploration, La Jolla, CA 92037, USA
| | - Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton 3240, New Zealand
| | - Margaret E Hunter
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL 32653, USA
| | - Johannes Karstensen
- Department of Physical Oceanography, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
| | - Christine M Laney
- Science department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - Margaret Leinen
- Geosciences Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Paula Mabee
- Observatory Leadership department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - James A Macklin
- Botany and Biodiversity Informatics, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario K1A 0C6, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Nicolas Pade
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
| | | | - Lori Phillips
- Agriculture and Agri-Food Canada (AAFC), Harrow N0R 1G0, Ontario, Canada
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Ioulia Santi
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Heraklion GR71003, Greece
| | - Dmitry Schigel
- GBIF | Global Biodiversity Information Facility, Copenhagen DK-2100, Denmark
| | - Lynn M Schriml
- Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alice Soccodato
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
| | - Saara Suominen
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Katherine M Thibault
- Science department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | | | | | | | - Ramona Walls
- Data Science department, Critical Path Institute, Tucson, AZ 85718, USA
| | - Pier Luigi Buttigieg
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Information, Data and Computer Center, Helmholtz Metadata Collaboration/GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
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5
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Bednaršek N, Carter BR, McCabe RM, Feely RA, Howard E, Chavez FP, Elliott M, Fisher JL, Jahncke J, Siegrist Z. Pelagic calcifiers face increased mortality and habitat loss with warming and ocean acidification. Ecol Appl 2022; 32:e2674. [PMID: 35584131 PMCID: PMC9786838 DOI: 10.1002/eap.2674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 06/15/2023]
Abstract
Global change is impacting the oceans in an unprecedented way, and multiple lines of evidence suggest that species distributions are changing in space and time. There is increasing evidence that multiple environmental stressors act together to constrain species habitat more than expected from warming alone. Here, we conducted a comprehensive study of how temperature and aragonite saturation state act together to limit Limacina helicina, globally distributed pteropods that are ecologically important pelagic calcifiers and an indicator species for ocean change. We co-validated three different approaches to evaluate the impact of ocean warming and acidification (OWA) on the survival and distribution of this species in the California Current Ecosystem. First, we used colocated physical, chemical, and biological data from three large-scale west coast cruises and regional time series; second, we conducted multifactorial experimental incubations to evaluate how OWA impacts pteropod survival; and third, we validated the relationships we found against global distributions of pteropods and carbonate chemistry. OWA experimental work revealed mortality increases under OWA, while regional habitat suitability indices and global distributions of L. helicina suggest that a multi-stressor framework is essential for understanding pteropod distributions. In California Current Ecosystem habitats, where pteropods are living close to their thermal maximum already, additional warming and acidification through unabated fossil fuel emissions (RCP 8.5) are expected to dramatically reduce habitat suitability.
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Affiliation(s)
- Nina Bednaršek
- Marine Biological StationNational Institute for BiologyLjubljanaSlovenia
- Cooperative Institute for Marine Resources StudiesOregon State UniversityNewportOregonUSA
| | - Brendan R. Carter
- Cooperative Institute for Climate, Ocean, and Ecosystem StudiesUniversity of WashingtonSeattleWashingtonUSA
- NOAA Pacific Marine Environmental LaboratorySeattleWashingtonUSA
| | - Ryan M. McCabe
- Cooperative Institute for Climate, Ocean, and Ecosystem StudiesUniversity of WashingtonSeattleWashingtonUSA
- NOAA Pacific Marine Environmental LaboratorySeattleWashingtonUSA
| | - Richard A. Feely
- Cooperative Institute for Climate, Ocean, and Ecosystem StudiesUniversity of WashingtonSeattleWashingtonUSA
| | - Evan Howard
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
| | | | | | - Jennifer L. Fisher
- Cooperative Institute for Marine Resources StudiesOregon State UniversityNewportOregonUSA
| | - Jaime Jahncke
- Point Blue Conservation SciencePetalumaCaliforniaUSA
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6
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Lamy T, Pitz KJ, Chavez FP, Yorke CE, Miller RJ. Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Sci Rep 2021; 11:14439. [PMID: 34262101 PMCID: PMC8280230 DOI: 10.1038/s41598-021-93859-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000-2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.
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Affiliation(s)
- Thomas Lamy
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA.
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Sète, France.
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA
| | | | - Christie E Yorke
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Robert J Miller
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
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7
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Choi CJ, Jimenez V, Needham DM, Poirier C, Bachy C, Alexander H, Wilken S, Chavez FP, Sudek S, Giovannoni SJ, Worden AZ. Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans. Front Microbiol 2020; 11:542372. [PMID: 33101224 PMCID: PMC7554337 DOI: 10.3389/fmicb.2020.542372] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Much is known about how broad eukaryotic phytoplankton groups vary according to nutrient availability in marine ecosystems. However, genus- and species-level dynamics are generally unknown, although important given that adaptation and acclimation processes differentiate at these levels. We examined phytoplankton communities across seasonal cycles in the North Atlantic (BATS) and under different trophic conditions in the eastern North Pacific (ENP), using phylogenetic classification of plastid-encoded 16S rRNA amplicon sequence variants (ASVs) and other methodologies, including flow cytometric cell sorting. Prasinophytes dominated eukaryotic phytoplankton amplicons during the nutrient-rich deep-mixing winter period at BATS. During stratification (‘summer’) uncultured dictyochophytes formed ∼35 ± 10% of all surface plastid amplicons and dominated those from stramenopile algae, whereas diatoms showed only minor, ephemeral contributions over the entire year. Uncultured dictyochophytes also comprised a major fraction of plastid amplicons in the oligotrophic ENP. Phylogenetic reconstructions of near-full length 16S rRNA sequences established 11 uncultured Dictyochophyte Environmental Clades (DEC). DEC-I and DEC-VI dominated surface dictyochophytes under stratification at BATS and in the ENP, and DEC-IV was also important in the latter. Additionally, although less common at BATS, Florenciella-related clades (FC) were prominent at depth in the ENP. In both ecosystems, pelagophytes contributed notably at depth, with PEC-VIII (Pelagophyte Environmental Clade) and (cultured) Pelagomonas calceolata being most important. Q-PCR confirmed the near absence of P. calceolata at the surface of the same oligotrophic sites where it reached ∼1,500 18S rRNA gene copies ml–1 at the DCM. To further characterize phytoplankton present in our samples, we performed staining and at-sea single-cell sorting experiments. Sequencing results from these indicated several uncultured dictyochophyte clades are comprised of predatory mixotrophs. From an evolutionary perspective, these cells showed both conserved and unique features in the chloroplast genome. In ENP metatranscriptomes we observed high expression of multiple chloroplast genes as well as expression of a selfish element (group II intron) in the psaA gene. Comparative analyses across the Pacific and Atlantic sites support the conclusion that predatory dictyochophytes thrive under low nutrient conditions. The observations that several uncultured dictyochophyte lineages are seemingly capable of photosynthesis and predation, raises questions about potential shifts in phytoplankton trophic roles associated with seasonality and long-term ocean change.
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Affiliation(s)
- Chang Jae Choi
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Valeria Jimenez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - David M Needham
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Harriet Alexander
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Susanne Wilken
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
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8
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Reji L, Tolar BB, Chavez FP, Francis CA. Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System. Front Microbiol 2020; 11:1075. [PMID: 32523584 PMCID: PMC7261934 DOI: 10.3389/fmicb.2020.01075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/29/2020] [Indexed: 11/23/2022] Open
Abstract
Coastal upwelling regions are hotspots of biological productivity, supporting diverse communities of microbial life and metabolisms. Monterey Bay (MB), a coastal ocean embayment in central California, experiences seasonal upwelling of cold, nutrient-rich waters that sustain episodes of high phytoplankton production in surface waters. While productivity in surface waters is intimately linked to metabolisms of diverse communities of Archaea and Bacteria, a comprehensive understanding of the microbial community in MB is missing thus far, particularly in relation to the distinct hydrographic seasons characteristic of the MB system. Here we present the results of a 2-year microbial time-series survey in MB, investigating community composition and structure across spatiotemporal gradients. In deciphering these patterns, we used unique sequence variants (SVs) of the 16S rRNA gene (V4–V5 region), complemented with metagenomes and metatranscriptomes representing multiple depth profiles. We found clear depth-differentiation and recurring seasonal abundance patterns within planktonic communities, particularly when analyzed at finer taxonomic levels. Compositional changes were more pronounced in the upper 0–40 m of the water column, whereas deeper depths were characterized by temporally stable populations. In accordance with the dynamic nutrient profiles, the system appears to change from a Bacteroidetes- and Rhodobacterales-dominated upwelling period to an oceanic season dominated by oligotrophic groups such as SAR11 and picocyanobacteria. The cascade of environmental changes brought about by upwelling and relaxation events thus impacts microbial community structure in the bay, with important implications for the temporal variability of nutrient and energy fluxes within the MB ecosystem. Our observations emphasize the need for continued monitoring of planktonic microbial communities in order to predict and manage the behavior of this sensitive marine sanctuary ecosystem, over projected intensification of upwelling in the region.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Francisco P Chavez
- Biological Oceanography Group, Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, United States
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9
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Djurhuus A, Closek CJ, Kelly RP, Pitz KJ, Michisaki RP, Starks HA, Walz KR, Andruszkiewicz EA, Olesin E, Hubbard K, Montes E, Otis D, Muller-Karger FE, Chavez FP, Boehm AB, Breitbart M. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nat Commun 2020; 11:254. [PMID: 31937756 PMCID: PMC6959347 DOI: 10.1038/s41467-019-14105-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/12/2019] [Indexed: 02/02/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies. Increasingly, eDNA is being used to infer ecological interactions. Here the authors sample eDNA over 18 months in a marine environment and use co-occurrence network analyses to infer potential interactions among organisms from microbes to mammals, testing how they change over time in response to oceanographic factors.
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Affiliation(s)
- Anni Djurhuus
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.
| | - Collin J Closek
- Stanford Center for Ocean Solutions, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA. .,Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA.
| | - Ryan P Kelly
- University of Washington, School of Marine and Environmental Affairs, 3707 Brooklyn Ave, Seattle, WA, 98105, USA
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Reiko P Michisaki
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Hilary A Starks
- Stanford Center for Ocean Solutions, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA.,Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Kristine R Walz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Elizabeth A Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Emily Olesin
- Florida Fish and Wildlife Research Conservation-Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL, 33701, USA
| | - Katherine Hubbard
- Florida Fish and Wildlife Research Conservation-Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL, 33701, USA
| | - Enrique Montes
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Daniel Otis
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Frank E Muller-Karger
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Mya Breitbart
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.
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10
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Ryan JP, Cline DE, Joseph JE, Margolina T, Santora JA, Kudela RM, Chavez FP, Pennington JT, Wahl C, Michisaki R, Benoit-Bird K, Forney KA, Stimpert AK, DeVogelaere A, Black N, Fischer M. Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific. PLoS One 2019; 14:e0222456. [PMID: 31525231 PMCID: PMC6746543 DOI: 10.1371/journal.pone.0222456] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/30/2019] [Indexed: 11/20/2022] Open
Abstract
This study examines the occurrence of humpback whale (Megaptera novaeangliae) song in the northeast Pacific from three years of continuous recordings off central California (36.713°N, 122.186°W). Song is prevalent in this feeding and migratory habitat, spanning nine months of the year (September-May), peaking in winter (November-January), and reaching a maximum of 86% temporal coverage (during November 2017). From the rise of song in fall through the end of peak occurrence in winter, song length increases significantly from month to month. The seasonal peak in song coincides with the seasonal trough in day length and sighting-based evidence of whales leaving Monterey Bay, consistent with seasonal migration. During the seasonal song peak, diel variation shows maximum occurrence at night (69% of the time), decreasing during dawn and dusk (52%), and further decreasing with increasing solar elevation during the day, reaching a minimum near solar noon (30%). Song occurrence increased 44% and 55% between successive years. Sighting data within the acoustic detection range of the hydrophone indicate that variation in local population density was an unlikely cause of this large interannual variation. Hydrographic data and modeling of acoustic transmission indicate that changes in neither habitat occupancy nor acoustic transmission were probable causes. Conversely, the positive interannual trend in song paralleled major ecosystem variations, including similarly large positive trends in wind-driven upwelling, primary productivity, and krill abundance. Further, the lowest song occurrence during the first year coincided with anomalously warm ocean temperatures and an extremely toxic harmful algal bloom that affected whales and other marine mammals in the region. These major ecosystem variations may have influenced the health and behavior of humpback whales during the study period.
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Affiliation(s)
- John P. Ryan
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Danelle E. Cline
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - John E. Joseph
- Department of Oceanography, Naval Postgraduate School, Monterey, California, United States of America
| | - Tetyana Margolina
- Department of Oceanography, Naval Postgraduate School, Monterey, California, United States of America
| | - Jarrod A. Santora
- Department of Applied Mathematics, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Raphael M. Kudela
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Francisco P. Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - J. Timothy Pennington
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Christopher Wahl
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Reiko Michisaki
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Kelly Benoit-Bird
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Karin A. Forney
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Moss Landing, California, United States of America
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, United States of America
| | - Alison K. Stimpert
- Bioacoustics/Vertebrate Ecology, San Jose State University, Moss Landing Marine Laboratories, Moss Landing, California, United States of America
| | - Andrew DeVogelaere
- Monterey Bay National Marine Sanctuary, National Ocean Service, National Oceanic and Atmospheric Administration, Monterey, California, United States of America
| | - Nancy Black
- Monterey Bay Whale Watch, Monterey, California, United States of America
| | - Mark Fischer
- Aguasonic Acoustics, Santa Clara, California, United States of America
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11
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Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
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12
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Northcott D, Sevadjian J, Sancho-Gallegos DA, Wahl C, Friederich J, Chavez FP. Impacts of urban carbon dioxide emissions on sea-air flux and ocean acidification in nearshore waters. PLoS One 2019; 14:e0214403. [PMID: 30917190 PMCID: PMC6436797 DOI: 10.1371/journal.pone.0214403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/12/2019] [Indexed: 11/28/2022] Open
Abstract
Greatly enhanced atmospheric carbon dioxide (CO2) levels relative to well-mixed marine air are observed during periods of offshore winds at coastal sensor platforms in Monterey Bay, California, USA. The highest concentrations originate from urban and agricultural areas, are driven by diurnal winds, and peak in the early morning. These enhanced atmospheric levels can be detected across a ~100km wide nearshore area and represent a significant addition to total oceanic CO2 uptake. A global estimate puts the added sea-air flux of CO2 from these greatly enhanced atmospheric CO2 levels at 25 million tonnes, roughly 1% of the ocean’s annual CO2 uptake. The increased uptake over the 100 km coastal swath is of order 20%, indicating a potentially large impact on ocean acidification in productive coastal waters.
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Affiliation(s)
- Devon Northcott
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
- * E-mail: (FPC); (DN)
| | - Jeff Sevadjian
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
- Scripps Institution of Oceanography, La Jolla, CA, United States of America
| | - Diego A. Sancho-Gallegos
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
- Stanford University, Stanford, CA, United States of America
| | - Chris Wahl
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Jules Friederich
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Francisco P. Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
- * E-mail: (FPC); (DN)
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13
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Zhang Y, Rueda C, Kieft B, Ryan JP, Wahl C, O’Reilly TC, Maughan T, Chavez FP. Autonomous tracking of an oceanic thermal front by a Wave Glider. J FIELD ROBOT 2019. [DOI: 10.1002/rob.21862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yanwu Zhang
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Carlos Rueda
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Brian Kieft
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - John P. Ryan
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Christopher Wahl
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Thomas C. O’Reilly
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Thom Maughan
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
| | - Francisco P. Chavez
- Engineering Division, Monterey Bay Aquarium Research Institute Moss Landing California
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14
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Branch A, Flexas MM, Claus B, Thompson AF, Zhang Y, Clark EB, Chien S, Fratantoni DM, Kinsey JC, Hobson B, Kieft B, Chavez FP. Front delineation and tracking with multiple underwater vehicles. J FIELD ROBOT 2018. [DOI: 10.1002/rob.21853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrew Branch
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadena California
| | - Mar M. Flexas
- Division of Geological and Planetary Sciences, California Institute of TechnologyPasadena California
| | - Brian Claus
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanography InstitutionWoods Hole Massachusetts
| | - Andrew F. Thompson
- Division of Geological and Planetary Sciences, California Institute of TechnologyPasadena California
| | - Yanwu Zhang
- Monterey Bay Aquarium Research InstituteMoss Landing California
| | - Evan B. Clark
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadena California
| | - Steve Chien
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadena California
| | | | - James C. Kinsey
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanography InstitutionWoods Hole Massachusetts
| | - Brett Hobson
- Monterey Bay Aquarium Research InstituteMoss Landing California
| | - Brian Kieft
- Monterey Bay Aquarium Research InstituteMoss Landing California
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15
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Muller-Karger FE, Miloslavich P, Bax NJ, Simmons S, Costello MJ, Sousa Pinto I, Canonico G, Turner W, Gill M, Montes E, Best BD, Pearlman J, Halpin P, Dunn D, Benson A, Martin CS, Weatherdon LV, Appeltans W, Provoost P, Klein E, Kelble CR, Miller RJ, Chavez FP, Iken K, Chiba S, Obura D, Navarro LM, Pereira HM, Allain V, Batten S, Benedetti-Checchi L, Duffy JE, Kudela RM, Rebelo LM, Shin Y, Geller G. Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks. Front Mar Sci 2018; 5. [PMID: 0 DOI: 10.3389/fmars.2018.00211] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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16
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Ren AS, Chai F, Xue H, Anderson DM, Chavez FP. A Sixteen-year Decline in Dissolved Oxygen in the Central California Current. Sci Rep 2018; 8:7290. [PMID: 29740053 PMCID: PMC5940839 DOI: 10.1038/s41598-018-25341-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/11/2018] [Indexed: 11/13/2022] Open
Abstract
A potential consequence of climate change is global decrease in dissolved oxygen at depth in the oceans due to changes in the balance of ventilation, mixing, respiration, and photosynthesis. We present hydrographic cruise observations of declining dissolved oxygen collected along CalCOFI Line 66.7 (Line 67) off of Monterey Bay, in the Central California Current region, and investigate likely mechanisms. Between 1998 and 2013, dissolved oxygen decreased at the mean rate of 1.92 µmol kg−1 year−1 on σθ 26.6–26.8 kg m−3 isopycnals (250–400 m), translating to a 40% decline from initial concentrations. Two cores of elevated dissolved oxygen decline at 130 and 240 km from shore, which we suggest are a California Undercurrent and a California Current signal respectively, occurred on σθ ranges of 26.0–26.8 kg m−3 (100–400 m). A box model suggests that small annual changes in dissolved oxygen in source regions are sufficient to be the primary driver of the mid-depth declines. Variation in dissolved oxygen at the bottom of the surface mixed layer suggests that there is also a signal of increased local remineralization.
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Affiliation(s)
- Alice S Ren
- School of Marine Sciences, University of Maine, Orono, Maine, USA. .,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA.
| | - Fei Chai
- School of Marine Sciences, University of Maine, Orono, Maine, USA
| | - Huijie Xue
- School of Marine Sciences, University of Maine, Orono, Maine, USA
| | - David M Anderson
- Monterey Bay Aquarium Research Institute, Moss Landing, California, USA
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17
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Breitburg D, Levin LA, Oschlies A, Grégoire M, Chavez FP, Conley DJ, Garçon V, Gilbert D, Gutiérrez D, Isensee K, Jacinto GS, Limburg KE, Montes I, Naqvi SWA, Pitcher GC, Rabalais NN, Roman MR, Rose KA, Seibel BA, Telszewski M, Yasuhara M, Zhang J. Declining oxygen in the global ocean and coastal waters. Science 2018; 359:359/6371/eaam7240. [DOI: 10.1126/science.aam7240] [Citation(s) in RCA: 1096] [Impact Index Per Article: 182.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.
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18
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Andruszkiewicz EA, Starks HA, Chavez FP, Sassoubre LM, Block BA, Boehm AB. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS One 2017; 12:e0176343. [PMID: 28441466 PMCID: PMC5404852 DOI: 10.1371/journal.pone.0176343] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/10/2017] [Indexed: 02/03/2023] Open
Abstract
Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.
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Affiliation(s)
- Elizabeth A. Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Hilary A. Starks
- Center for Ocean Solutions, Stanford University, Stanford, CA, United States of America
| | - Francisco P. Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Lauren M. Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Barbara A. Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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19
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Kroeker KJ, Sanford E, Rose JM, Blanchette CA, Chan F, Chavez FP, Gaylord B, Helmuth B, Hill TM, Hofmann GE, McManus MA, Menge BA, Nielsen KJ, Raimondi PT, Russell AD, Washburn L. Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability. Ecol Lett 2016; 19:771-779. [PMID: 27151381 DOI: 10.111/ele.12613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/12/2016] [Accepted: 04/04/2016] [Indexed: 05/25/2023]
Abstract
Although theory suggests geographic variation in species' performance is determined by multiple niche parameters, little consideration has been given to the spatial structure of interacting stressors that may shape local and regional vulnerability to global change. Here, we use spatially explicit mosaics of carbonate chemistry, food availability and temperature spanning 1280 km of coastline to test whether persistent, overlapping environmental mosaics mediate the growth and predation vulnerability of a critical foundation species, the mussel Mytilus californianus. We find growth was highest and predation vulnerability was lowest in dynamic environments with frequent exposure to low pH seawater and consistent food. In contrast, growth was lowest and predation vulnerability highest when exposure to low pH seawater was decoupled from high food availability, or in exceptionally warm locations. These results illustrate how interactions among multiple drivers can cause unexpected, yet persistent geographic mosaics of species performance, interactions and vulnerability to environmental change.
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Affiliation(s)
- Kristy J Kroeker
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric Sanford
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Jeremy M Rose
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Carol A Blanchette
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Francis Chan
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | | | - Brian Gaylord
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Brian Helmuth
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, USA
| | - Tessa M Hill
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA
- Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Margaret A McManus
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Bruce A Menge
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Karina J Nielsen
- Romberg Tiburon Center, San Francisco State University, San Francisco, CA, USA
| | - Peter T Raimondi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ann D Russell
- Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
| | - Libe Washburn
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Geography, University of California Santa Barbara, Santa Barbara, CA, USA
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20
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Kroeker KJ, Sanford E, Rose JM, Blanchette CA, Chan F, Chavez FP, Gaylord B, Helmuth B, Hill TM, Hofmann GE, McManus MA, Menge BA, Nielsen KJ, Raimondi PT, Russell AD, Washburn L. Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability. Ecol Lett 2016; 19:771-9. [PMID: 27151381 DOI: 10.1111/ele.12613] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/12/2016] [Accepted: 04/04/2016] [Indexed: 11/28/2022]
Abstract
Although theory suggests geographic variation in species' performance is determined by multiple niche parameters, little consideration has been given to the spatial structure of interacting stressors that may shape local and regional vulnerability to global change. Here, we use spatially explicit mosaics of carbonate chemistry, food availability and temperature spanning 1280 km of coastline to test whether persistent, overlapping environmental mosaics mediate the growth and predation vulnerability of a critical foundation species, the mussel Mytilus californianus. We find growth was highest and predation vulnerability was lowest in dynamic environments with frequent exposure to low pH seawater and consistent food. In contrast, growth was lowest and predation vulnerability highest when exposure to low pH seawater was decoupled from high food availability, or in exceptionally warm locations. These results illustrate how interactions among multiple drivers can cause unexpected, yet persistent geographic mosaics of species performance, interactions and vulnerability to environmental change.
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Affiliation(s)
- Kristy J Kroeker
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric Sanford
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA.,Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Jeremy M Rose
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Carol A Blanchette
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Francis Chan
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | | | - Brian Gaylord
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA.,Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Brian Helmuth
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA, USA
| | - Tessa M Hill
- Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA, USA.,Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Margaret A McManus
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Bruce A Menge
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Karina J Nielsen
- Romberg Tiburon Center, San Francisco State University, San Francisco, CA, USA
| | - Peter T Raimondi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ann D Russell
- Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA
| | - Libe Washburn
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA.,Department of Geography, University of California Santa Barbara, Santa Barbara, CA, USA
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Hughes BB, Levey MD, Fountain MC, Carlisle AB, Chavez FP, Gleason MG. Climate mediates hypoxic stress on fish diversity and nursery function at the land-sea interface. Proc Natl Acad Sci U S A 2015; 112:8025-30. [PMID: 26056293 PMCID: PMC4491771 DOI: 10.1073/pnas.1505815112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coastal ecosystems provide numerous important ecological services, including maintenance of biodiversity and nursery grounds for many fish species of ecological and economic importance. However, human population growth has led to increased pollution, ocean warming, hypoxia, and habitat alteration that threaten ecosystem services. In this study, we used long-term datasets of fish abundance, water quality, and climatic factors to assess the threat of hypoxia and the regulating effects of climate on fish diversity and nursery conditions in Elkhorn Slough, a highly eutrophic estuary in central California (United States), which also serves as a biodiversity hot spot and critical nursery grounds for offshore fisheries in a broader region. We found that hypoxic conditions had strong negative effects on extent of suitable fish habitat, fish species richness, and abundance of the two most common flatfish species, English sole (Parophrys vetulus) and speckled sanddab (Citharichthys stigmaeus). The estuary serves as an important nursery ground for English sole, making this species vulnerable to anthropogenic threats. We determined that estuarine hypoxia was associated with significant declines in English sole nursery habitat, with cascading effects on recruitment to the offshore adult population and fishery, indicating that human land use activities can indirectly affect offshore fisheries. Estuarine hypoxic conditions varied spatially and temporally and were alleviated by strengthening of El Niño conditions through indirect pathways, a consistent result in most estuaries across the northeast Pacific. These results demonstrate that changes to coastal land use and climate can fundamentally alter the diversity and functioning of coastal nurseries and their adjacent ocean ecosystems.
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Affiliation(s)
- Brent B Hughes
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060;
| | | | - Monique C Fountain
- Elkhorn Slough National Estuarine Research Reserve, Watsonville, CA 95076
| | - Aaron B Carlisle
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950
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Sudek S, Everroad RC, Gehman ALM, Smith JM, Poirier CL, Chavez FP, Worden AZ. Cyanobacterial distributions along a physico-chemical gradient in the Northeastern Pacific Ocean. Environ Microbiol 2015; 17:3692-707. [PMID: 25522910 DOI: 10.1111/1462-2920.12742] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 12/11/2022]
Abstract
The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and covariance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. An inter-annual pattern was delineated in the dynamic transition zone where upwelled and eastern boundary current waters mix, and two new Synechococcus clades, Eastern Pacific Clade (EPC) 1 and EPC2, were identified. By applying state-of-the-art phylogenetic analysis tools to bar-coded 16S amplicon datasets, we observed higher abundance of Prochlorococcus high-light I (HLI) and low-light I (LLI) in years when more oligotrophic water intruded farther inshore, while under stronger upwelling Synechococcus I and IV dominated. However, contributions of some cyanobacterial clades were proportionally relatively constant, e.g. Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than previously reported. The phylogenetic precision of our 16S rRNA gene analytical approach and depth of bar-coded sequencing also facilitated detection of clades at low abundance in unexpected places. These include Prochlorococcus at the coast and Cyanobium-related sequences offshore, although it remains unclear whether these came from resident or potentially advected cells. Our study enhances understanding of cyanobacterial distributions in an ecologically important eastern boundary system.
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Affiliation(s)
- Sebastian Sudek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - R Craig Everroad
- Exobiology Branch, NASA Ames Research Center, MS 239-4, Moffett Field, CA, 94035, USA
| | - Alyssa-Lois M Gehman
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Camille L Poirier
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
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Abstract
Nitrification, the microbial oxidation of ammonium to nitrate, is a central part of the nitrogen cycle. In the ocean’s surface layer, the process alters the distribution of inorganic nitrogen species available to phytoplankton and produces nitrous oxide. A widely held idea among oceanographers is that nitrification is inhibited by light in the ocean. However, recent evidence that the primary organisms involved in nitrification, the ammonia-oxidizing archaea (AOA), are present and active throughout the surface ocean has challenged this idea. Here we show, through field experiments coupling molecular genetic and biogeochemical approaches, that competition for ammonium with phytoplankton is the strongest regulator of nitrification in the photic zone. During multiday experiments at high irradiance a single ecotype of AOA remained active in the presence of rapidly growing phytoplankton. Over the course of this three day experiment, variability in the intensity of competition with phytoplankton caused nitrification rates to decline from those typical of the lower photic zone (60 nmol L−1 d−1) to those in well-lit layers (<1 nmol L−1 d−1). During another set of experiments, nitrification rates exhibited a diel periodicity throughout much of the photic zone, with the highest rates occurring at night when competition with phytoplankton is lowest. Together, the results of our experiments indicate that nitrification rates in the photic zone are more strongly regulated by competition with phytoplankton for ammonium than they are by light itself. This finding advances our ability to model the impact of nitrification on estimates of new primary production, and emphasizes the need to more strongly consider the effects of organismal interactions on nutrient standing stocks and biogeochemical cycling in the surface of the ocean.
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Affiliation(s)
- Jason M. Smith
- Research Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- Department of Environmental Earth System Science, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Francisco P. Chavez
- Research Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Christopher A. Francis
- Department of Environmental Earth System Science, Stanford University, Stanford, California, United States of America
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Xu Y, Chai F, Rose KA, Ñiquen C. M, Chavez FP. Environmental influences on the interannual variation and spatial distribution of Peruvian anchovy (Engraulis ringens) population dynamics from 1991 to 2007: A three-dimensional modeling study. Ecol Modell 2013. [DOI: 10.1016/j.ecolmodel.2013.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Paerl RW, Turk KA, Beinart RA, Chavez FP, Zehr JP. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR. Environ Microbiol 2011; 14:580-93. [PMID: 21955724 DOI: 10.1111/j.1462-2920.2011.02594.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synechococcus is a cosmopolitan marine cyanobacterial genus, and is often the most abundant picocyanobacterial genus in coastal waters. Little is known about Synechococcus seasonal dynamics in coastal zones highly impacted by upwelling. This was investigated by collecting seasonal samples from an upwelling-impacted Monterey Bay (MB) monitoring station M0, in parallel with measurements of oceanographic conditions during 2006-2008. Synechococcus abundances were determined using quantitative PCR (qPCR) assays and flow cytometry (FCM). A new qPCR assay was designed to target dominant Synechococcus in MB using the rbcL gene, while previously designed assays targeted distinct phylotypes (called narB subgroups) with the narB gene. The rbcL qPCR assay successfully tracked abundant Synechococcus in MB, accounting for on average 89% (± 57%) of FCM-based counts. Annual spring upwelling caused decreases in Synechococcus and narB subgroup abundances. Differences in narB subgroup abundance maxima and abundance patterns support the view that subgroups differ in their ecologies, including subgroup D_C1, which seems to specifically thrive in coastal waters. Correlations between narB subgroup abundances and measured environmental variables were similar among the subgroups. Therefore, non-measured environmental factors (e.g. metals, mortality) likely had different influences on subgroups, which led to their distinct abundance patterns at M0.
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Affiliation(s)
- Ryan W Paerl
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP, Zehr JP. Differential distributions of synechococcus subgroups across the california current system. Front Microbiol 2011; 2:59. [PMID: 21833315 PMCID: PMC3153035 DOI: 10.3389/fmicb.2011.00059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/15/2011] [Indexed: 01/08/2023] Open
Abstract
Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.
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Affiliation(s)
- Ryan W Paerl
- Department of Ocean Sciences, University of California Santa Cruz Santa Cruz, CA, USA
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28
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Abstract
Marine photosynthetic plankton are responsible for approximately 50 petagrams (10(15)) of carbon per year of net primary production, an amount equivalent to that on land. This primary production supports essentially all life in the oceans and profoundly affects global biogeochemical cycles and climate. This review discusses the general distribution of primary production in the sea, the processes that regulate this distribution, and how marine primary production is sensitive to climate variability and change. Statistical modes of ocean variability and their characteristic interannual to multi-decadal timescales over the last century are described. Recent in situ and satellite time-series of primary production can be clearly linked to interannual ocean variability. Global marine primary production appears to have increased over the past several decades in association with multi-decadal variations. A paleoclimate record extends discussion to the centennial scale, providing contrasting insights into how marine primary production might vary in the future.
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Affiliation(s)
- Francisco P Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA.
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29
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Abstract
Observations of the 1982-1983 El Niño make it possible to relate the anomalous ocean conditions to specific biological responses. In October 1982 upwelling ecosystems in the eastern equatorial Pacific began a series of transitions from the normal highly productive condition to greatly reduced productivity. The highly productive condition had returned by July 1983. Nutrients, phytoplankton biomass, and primary productivity are clearly regulated by the physical changes of El Niño. Evidence from 1982 and 1983 also suggests effects on higher organisms such as fish, seabirds, and marine mammals, but several more years of observation are required to accurately determine the magnitude of the consequences on these higher trophic levels.
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Conaway CH, Black FJ, Gault-Ringold M, Pennington JT, Chavez FP, Flegal AR. Dimethylmercury in coastal upwelling waters, Monterey Bay, California. Environ Sci Technol 2009; 43:1305-1309. [PMID: 19350895 DOI: 10.1021/es802705t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Depth profiles of dimethylmercury (DMHg) concentration were determined at nearshore to offshore sites in Monterey Bay, California. The onset of spring upwelling in the bay was accompanied by increases in DMHg concentrations. Profiles show DMHg increasing gradually with depth in fall and winter from <0.03 pM at the surface to 0.5 pM at 200 m. During the spring, DMHg concentrations increased between 30 and 100 m, first within Monterey Bay, then offshore. This change was accompanied by an increase in DMHg concentrations in the surface water DMHg between fall/winter (<0.03 pM) and spring (0.06-0.29 pM). Microbial activity associated with the remineralization of sinking organic matter produced by the high primary production in the bay may result in the relatively high DMHg in subsurface water in the bay, which when upwelled may facilitate the incorporation of organomercury into biota. As a result, productive coastal upwelling areas may represent an important source of methylated mercury to surface waters, and thus be an important source of mercury to marine ecosystems.
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Affiliation(s)
- Christopher H Conaway
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA.
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Coale KH, Johnson KS, Fitzwater SE, Gordon RM, Tanner S, Chavez FP, Ferioli L, Sakamoto C, Rogers P, Millero F, Steinberg P, Nightingale P, Cooper D, Cochlan WP, Landry MR, Constantinou J, Rollwagen G, Trasvina A, Kudela R. A massive phytoplankton bloom induced by an ecosystem-scale iron fertilization experiment in the equatorial Pacific Ocean. Nature 2008; 383:495 - 501. [PMID: 18680864 DOI: 10.1038/383495a0] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The seeding of an expanse of surface waters in the equatorial Pacific Ocean with low concentrations of dissolved iron triggered a massive phytoplankton bloom which consumed large quantities of carbon dioxide and nitrate that these microscopic plants cannot fully utilize under natural conditions. These and other observations provide unequivocal support for the hypothesis that phytoplankton growth in this oceanic region is limited by iron bioavailability.
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Affiliation(s)
- Vincent S Saba
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William and Mary, Rt. 1208 Greate Road, Gloucester Point, Virginia 23062, USA.
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Behrenfeld MJ, Worthington K, Sherrell RM, Chavez FP, Strutton P, McPhaden M, Shea DM. Controls on tropical Pacific Ocean productivity revealed through nutrient stress diagnostics. Nature 2006; 442:1025-8. [PMID: 16943835 DOI: 10.1038/nature05083] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 07/19/2006] [Indexed: 11/08/2022]
Abstract
In situ enrichment experiments have shown that the growth of bloom-forming diatoms in the major high-nitrate low-chlorophyll (HNLC) regions of the world's oceans is limited by the availability of iron. Yet even the largest of these manipulative experiments represents only a small fraction of an ocean basin, and the responses observed are strongly influenced by the proliferation of rare species rather than the growth of naturally dominant populations. Here we link unique fluorescence attributes of phytoplankton to specific physiological responses to nutrient stress, and use these relationships to evaluate the factors that constrain phytoplankton growth in the tropical Pacific Ocean on an unprecedented spatial scale. On the basis of fluorescence measurements taken over 12 years, we delineate three major ecophysiological regimes in this region. We find that iron has a key function in regulating phytoplankton growth in both HNLC and oligotrophic waters near the Equator and further south, whereas nitrogen and zooplankton grazing are the primary factors that regulate biomass production in the north. Application of our findings to the interpretation of satellite chlorophyll fields shows that productivity in the tropical Pacific basin may be 1.2-2.5 Pg C yr(-1) lower than previous estimates have suggested, a difference that is comparable to the global change in ocean production that accompanied the largest El Niño to La Niña transition on record.
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Affiliation(s)
- Michael J Behrenfeld
- Department of Botany and Plant Pathology, Cordley Hall 2082, Oregon State University, Corvallis, Oregon 97331-2902, USA.
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Ryan JP, Ueki I, Chao Y, Zhang H, Polito PS, Chavez FP. Western Pacific modulation of large phytoplankton blooms in the central and eastern equatorial Pacific. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/2005jg000084] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John P. Ryan
- Monterey Bay Aquarium Research Institute; Moss Landing California USA
| | - Iwao Ueki
- Japan Agency for Marine-Earth Science and Technology; Yokosuka Japan
| | - Yi Chao
- Jet Propulsion Laboratory; California Institute of Technology; Pasadena California USA
| | - Hongchun Zhang
- Jet Propulsion Laboratory; California Institute of Technology; Pasadena California USA
- Raytheon Information Technology and Scientific Services; Pasadena California USA
| | - Paulo S. Polito
- Instituto Oceanográfico da Universidade de São Paulo; Sao Paulo Brazil
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Hendricks MB, Bender ML, Barnett BA, Strutton P, Chavez FP. Triple oxygen isotope composition of dissolved O2in the equatorial Pacific: A tracer of mixing, production, and respiration. ACTA ACUST UNITED AC 2005. [DOI: 10.1029/2004jc002735] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Coale KH, Johnson KS, Chavez FP, Buesseler KO, Barber RT, Brzezinski MA, Cochlan WP, Millero FJ, Falkowski PG, Bauer JE, Wanninkhof RH, Kudela RM, Altabet MA, Hales BE, Takahashi T, Landry MR, Bidigare RR, Wang X, Chase Z, Strutton PG, Friederich GE, Gorbunov MY, Lance VP, Hilting AK, Hiscock MR, Demarest M, Hiscock WT, Sullivan KF, Tanner SJ, Gordon RM, Hunter CN, Elrod VA, Fitzwater SE, Jones JL, Tozzi S, Koblizek M, Roberts AE, Herndon J, Brewster J, Ladizinsky N, Smith G, Cooper D, Timothy D, Brown SL, Selph KE, Sheridan CC, Twining BS, Johnson ZI. Southern Ocean Iron Enrichment Experiment: Carbon Cycling in High- and Low-Si Waters. Science 2004; 304:408-14. [PMID: 15087542 DOI: 10.1126/science.1089778] [Citation(s) in RCA: 465] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.
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Affiliation(s)
- Kenneth H Coale
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039-9647, USA.
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Abstract
In the Pacific Ocean, air and ocean temperatures, atmospheric carbon dioxide, landings of anchovies and sardines, and the productivity of coastal and open ocean ecosystems have varied over periods of about 50 years. In the mid-1970s, the Pacific changed from a cool "anchovy regime" to a warm "sardine regime." A shift back to an anchovy regime occurred in the middle to late 1990s. These large-scale, naturally occurring variations must be taken into account when considering human-induced climate change and the management of ocean living resources.
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Affiliation(s)
- Francisco P Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA.
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Scholin CA, Gulland F, Doucette GJ, Benson S, Busman M, Chavez FP, Cordaro J, DeLong R, De Vogelaere A, Harvey J, Haulena M, Lefebvre K, Lipscomb T, Loscutoff S, Lowenstine LJ, Marin R, Miller PE, McLellan WA, Moeller PD, Powell CL, Rowles T, Silvagni P, Silver M, Spraker T, Trainer V, Van Dolah FM. Mortality of sea lions along the central California coast linked to a toxic diatom bloom. Nature 2000; 403:80-4. [PMID: 10638756 DOI: 10.1038/47481] [Citation(s) in RCA: 319] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over 400 California sea lions (Zalophus californianus) died and many others displayed signs of neurological dysfunction along the central California coast during May and June 1998. A bloom of Pseudo-nitzschia australis (diatom) was observed in the Monterey Bay region during the same period. This bloom was associated with production of domoic acid (DA), a neurotoxin that was also detected in planktivorous fish, including the northern anchovy (Engraulis mordax), and in sea lion body fluids. These and other concurrent observations demonstrate the trophic transfer of DA resulting in marine mammal mortality. In contrast to fish, blue mussels (Mytilus edulus) collected during the DA outbreak contained no DA or only trace amounts. Such findings reveal that monitoring of mussel toxicity alone does not necessarily provide adequate warning of DA entering the food web at levels sufficient to harm marine wildlife and perhaps humans.
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Affiliation(s)
- C A Scholin
- Monterey Bay Aquarium Research Institute, California 95039, USA.
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Chavez FP, Strutton PG, Friederich GE, Feely RA, Feldman GC, Foley DG, McPhaden MJ. Biological and chemical response of the equatorial pacific ocean to the 1997-98 El Nino. Science 1999; 286:2126-31. [PMID: 10591638 DOI: 10.1126/science.286.5447.2126] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
During the 1997-98 El Nino, the equatorial Pacific Ocean retained 0. 7 x 10(15) grams of carbon that normally would have been lost to the atmosphere as carbon dioxide. The surface ocean became impoverished in plant nutrients, and chlorophyll concentrations were the lowest on record. A dramatic recovery occurred in mid-1998, the system became highly productive, analogous to coastal environments, and carbon dioxide flux out of the ocean was again high. The spatial extent of the phytoplankton bloom that followed recovery from El Nino was the largest ever observed for the equatorial Pacific. These chemical and ecological perturbations were linked to changes in the upwelling of nutrient-enriched waters. The description and explanation of these dynamic changes would not have been possible without an observing system that combines biological, chemical, and physical sensors on moorings with remote sensing of chlorophyll.
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Affiliation(s)
- FP Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA. E-mail: . National Oceanic and Atmospheric Administration Pacific Marine Environmental Laboratory, 7600 Sand Point Way NE, Seattle, WA 98115, USA
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Abstract
An empirical correlation between marine barite (BaSO4) accumulation rate in core-top sediment samples from two equatorial Pacific transects (at 140°W and 110°W) and the estimated primary productivity of the overlying water column were used to evaluate glacial to interglacial changes in productivity. Fluctuations in barite accumulation rates down-core indicate that during glacial periods of the past 450,000 years, the productivity in the central and eastern equatorial Pacific was about two times that during intervening interglacial periods. This result is consistent with other evidence that productivity was high in the eastern and central equatorial Pacific during the last glacial.
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Affiliation(s)
- A Paytan
- A. Paytan and M. Kastner, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0212, USA. E-mail: F. P. Chavez, MBARI, Post Office Box 628, 7700 Sandholdt Road, Moss Landing, CA 95039-0628, USA
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44
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Abstract
The oceans play an important role in the geochemical cycle of methyl bromide (CH3Br), the major carrier of O3-destroying bromine to the stratosphere. The quantity of CH3Br produced annually in seawater is comparable to the amount entering the atmosphere each year from natural and anthropogenic sources. The production mechanism is unknown but may be biological. Most of this CH3Br is consumed in situ by hydrolysis or reaction with chloride. The size of the fraction which escapes to the atmosphere is poorly constrained; measurements in seawater and the atmosphere have been used to justify both a large oceanic CH3Br flux to the atmosphere and a small net ocean sink. Since the consumption reactions are extremely temperature-sensitive, small temperature variations have large effects on the CH3Br concentration in seawater, and therefore on the exchange between the atmosphere and the ocean. The net CH3Br flux is also sensitive to variations in the rate of CH3Br production. We have quantified these effects using a simple steady state mass balance model. When CH3Br production rates are linearly scaled with seawater chlorophyll content, this model reproduces the latitudinal variations in marine CH3Br concentrations observed in the east Pacific Ocean by Singh et al. [1983] and by Lobert et al. [1995]. The apparent correlation of CH3Br production with primary production explains the discrepancies between the two observational studies, strengthening recent suggestions that the open ocean is a small net sink for atmospheric CH3Br, rather than a large net source. The Southern Ocean is implicated as a possible large net source of CH3Br to the atmosphere. Since our model indicates that both the direction and magnitude of CH3Br exchange between the atmosphere and ocean are extremely sensitive to temperature and marine productivity, and since the rate of CH3Br production in the oceans is comparable to the rate at which this compound is introduced to the atmosphere, even small perturbations to temperature or productivity can modify atmospheric CH3Br. Therefore atmospheric CH3Br should be sensitive to climate conditions. Our modeling indicates that climate-induced CH3Br variations can be larger than those resulting from small (+/- 25%) changes in the anthropogenic source, assuming that this source comprises less than half of all inputs. Future measurements of marine CH3Br, temperature, and primary production should be combined with such models to determine the relationship between marine biological activity and CH3Br production. Better understanding of the biological term is especially important to assess the importance of non-anthropogenic sources to stratospheric ozone loss and the sensitivity of these sources to global climate change.
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Affiliation(s)
- A D Anbar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, USA
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Bates TS, Kiene RP, Wolfe GV, Matrai PA, Chavez FP, Buck KR, Blomquist BW, Cuhel RL. The cycling of sulfur in surface seawater of the northeast Pacific. ACTA ACUST UNITED AC 1994. [DOI: 10.1029/93jc02782] [Citation(s) in RCA: 168] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Scholin CA, Villac MC, Buck KR, Krupp JM, Powers DA, Fryxell GA, Chavez FP. Ribosomal DNA sequences discriminate among toxic and non-toxic Pseudonitzschia species. Nat Toxins 1994; 2:152-65. [PMID: 7952939 DOI: 10.1002/nt.2620020403] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cultured isolates of Pseudonitzschia australis Frenguelli, P. delicatissima (Cleve) Heiden, P. americana (Hasle) Fryxell, P. pungens (Grunow) Hasle, and P. pungens f. multiseries (Hasle) Hasle from Monterey Bay, California, were compared on the basis of their large-subunit ribosomal RNA gene (LsrDNA). Pseudonitzschia australis, P. pungens f. multiseries, and P. delicatissima were previously shown to produce the neurotoxin domoic acid; the remaining isolates are considered non-toxic. For each isolate approximately 800 base pairs of LsrDNA, encompassing both evolutionarily conserved and evolutionarily variable regions of the molecule, were amplified using the polymerase chain reaction (PCR) and sequenced. Phylogenetic trees generated by parsimony analysis of aligned sequences afford a preliminary view of the organisms genetic relationships. Species defined by morphological criteria are also distinguishable by LsrDNA sequence. Organisms known or suspected to produce domoic acid cluster at different termini on the phylogenetic tree. Two genetically distinct strains of P. australis and P. pungens were identified. Development of a restriction fragment length polymorphism (RFLP) assay of the LsrDNA is described. The RFLP assay discriminates each species, including distinguished strains of P. australis and P. pungens. The restriction test provides a rapid and convenient method for screening isolates' LsrDNA, facilitating further tests of the apparent positive correlation between Pseudonitzschia species' ribosomal gene signatures, morphology, and capacity to produce domoic acid.
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Affiliation(s)
- C A Scholin
- Monterey Bay Aquarium Research Institute, Pacific Grove, CA 93950
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Eppley RW, Chavez FP, Barber RT. Standing stocks of particulate carbon and nitrogen in the equatorial Pacific at 150°W. ACTA ACUST UNITED AC 1992. [DOI: 10.1029/91jc01386] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Thomsen HA, Buck KR, Chavez FP. Choanoflagellates of the Central California waters: Taxonomy, Morphology and species assemblages. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/00785326.1991.10429736] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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