1
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Weatherup EF, Carnegie RB, Strand AE, Sotka EE. Co-phylogeographic structure in a disease-causing parasite and its oyster host. Parasitology 2024:1-30. [PMID: 38769826 DOI: 10.1017/s0031182024000611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- E F Weatherup
- Virgina Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA, USA
| | - R B Carnegie
- Virgina Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA, USA
| | - A E Strand
- College of Charleston Marine Laboratory and Department of Biology, College of Charleston, 205 Fort Johnson Road, Charleston SC 29412, USA
| | - E E Sotka
- College of Charleston Marine Laboratory and Department of Biology, College of Charleston, 205 Fort Johnson Road, Charleston SC 29412, USA
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2
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McElwain JC, Matthaeus WJ, Barbosa C, Chondrogiannis C, O' Dea K, Jackson B, Knetge AB, Kwasniewska K, Nair R, White JD, Wilson JP, Montañez IP, Buckley YM, Belcher CM, Nogué S. Functional traits of fossil plants. New Phytol 2024; 242:392-423. [PMID: 38409806 DOI: 10.1111/nph.19622] [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] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/19/2023] [Indexed: 02/28/2024]
Abstract
A minuscule fraction of the Earth's paleobiological diversity is preserved in the geological record as fossils. What plant remnants have withstood taphonomic filtering, fragmentation, and alteration in their journey to become part of the fossil record provide unique information on how plants functioned in paleo-ecosystems through their traits. Plant traits are measurable morphological, anatomical, physiological, biochemical, or phenological characteristics that potentially affect their environment and fitness. Here, we review the rich literature of paleobotany, through the lens of contemporary trait-based ecology, to evaluate which well-established extant plant traits hold the greatest promise for application to fossils. In particular, we focus on fossil plant functional traits, those measurable properties of leaf, stem, reproductive, or whole plant fossils that offer insights into the functioning of the plant when alive. The limitations of a trait-based approach in paleobotany are considerable. However, in our critical assessment of over 30 extant traits we present an initial, semi-quantitative ranking of 26 paleo-functional traits based on taphonomic and methodological criteria on the potential of those traits to impact Earth system processes, and for that impact to be quantifiable. We demonstrate how valuable inferences on paleo-ecosystem processes (pollination biology, herbivory), past nutrient cycles, paleobiogeography, paleo-demography (life history), and Earth system history can be derived through the application of paleo-functional traits to fossil plants.
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Affiliation(s)
- Jennifer C McElwain
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - William J Matthaeus
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Catarina Barbosa
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | | | - Katie O' Dea
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Bea Jackson
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Antonietta B Knetge
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Kamila Kwasniewska
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Richard Nair
- School of Natural Sciences, Botany, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Joseph D White
- Department of Biology, Baylor University, Waco, 76798-7388, TX, USA
| | - Jonathan P Wilson
- Department of Environmental Studies, Haverford College, Haverford, Pennsylvania, 19041, PA, USA
| | - Isabel P Montañez
- UC Davis Institute of the Environment, University of California, Davis, CA, 95616, USA
- Department of Earth and Planetary Sciences, University of California, Davis, CA, 95616, USA
| | - Yvonne M Buckley
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | | | - Sandra Nogué
- Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
- CREAF, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
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3
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Edmunds PJ, Maritorena S, Burgess SC. Early post-settlement events, rather than settlement, drive recruitment and coral recovery at Moorea, French Polynesia. Oecologia 2024; 204:625-640. [PMID: 38418704 DOI: 10.1007/s00442-024-05517-y] [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: 01/12/2023] [Accepted: 01/20/2024] [Indexed: 03/02/2024]
Abstract
Understanding population dynamics is a long-standing objective of ecology, but the need for progress in this area has become urgent. For coral reefs, achieving this objective is impeded by a lack of information on settlement versus post-settlement events in determining recruitment and population size. Declines in coral abundance are often inferred to be associated with reduced densities of recruits, which could arise from mechanisms occurring at larval settlement, or throughout post-settlement stages. This study uses annual measurements from 2008 to 2021 of coral cover, the density of coral settlers (S), the density of small corals (SC), and environmental conditions, to evaluate the roles of settlement versus post-settlement events in determining rates of coral recruitment and changes in coral cover at Moorea, French Polynesia. Coral cover, S, SC, and the SC:S ratio (a proxy for post-settlement success), and environmental conditions, were used in generalized additive models (GAMs) to show that: (a) coral cover was more strongly related to SC and SC:S than S, and (b) SC:S was highest when preceded by cool seawater, low concentrations of Chlorophyll a, and low flow speeds, and S showed evidence of declining with elevated temperature. Together, these results suggest that changes in coral cover in Moorea are more strongly influenced by post-settlement events than settlement. The key to understanding coral community resilience may lie in elucidating the factors attenuating the bottleneck between settlers and small corals.
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Affiliation(s)
- Peter J Edmunds
- Department of Biology, California State University, Northridge, CA, 91330-8303, USA.
| | - Stéphane Maritorena
- Earth Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-3060, USA
| | - Scott C Burgess
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
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4
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Qin Y, Perraud V, Finlayson-Pitts BJ, Wingen LM. Peroxides on the Surface of Organic Aerosol Particles Using Matrix-Assisted Ionization in Vacuum (MAIV) Mass Spectrometry. Environ Sci Technol 2023; 57:14260-14268. [PMID: 37695633 PMCID: PMC10537442 DOI: 10.1021/acs.est.3c02895] [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] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Organic peroxides are key intermediates in the atmosphere but are challenging to detect, especially in the particle phase, due to their instability, which has led to substantial gaps in the understanding of their environmental effects. We demonstrate that matrix-assisted ionization in vacuum (MAIV) mass spectrometry (MS), which does not require an ionization source, enables in situ characterization of peroxides and other products in the surface layers of organic particles. Hydroxyl radical oxidation of glutaric acid particles yields hydroperoxides and organic peroxides, which were detected with signals of the same order of magnitude as the major, more stable products. Product identification is supported by MS/MS analysis, peroxide standards, and offline high-resolution MS. The peroxide signals relative to the stable carbonyl and alcohol products are significantly larger using MAIV compared to those in the offline bulk analysis. This is also the case for analysis using fast, online easy ambient sonic-spray ionization mass spectrometry. These studies demonstrate the advantage of MAIV for the real-time characterization of labile peroxides in the surface layers of solid particles. The presence of peroxides on the surface may be important for surface oxidation processes as well as for the toxicity of inhaled particles.
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Affiliation(s)
- Yiming Qin
- Department of Chemistry, University
of California, Irvine, California 92697-2025 United States
| | - Véronique Perraud
- Department of Chemistry, University
of California, Irvine, California 92697-2025 United States
| | | | - Lisa M. Wingen
- Department of Chemistry, University
of California, Irvine, California 92697-2025 United States
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5
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Paul R, Rogers TJ, Fullerton KM, Selci M, Cascone M, Stokes MH, Steen AD, de Moor JM, Chiodi A, Stefánsson A, Halldórsson SA, Ramirez CJ, Jessen GL, Barry PH, Cordone A, Giovannelli D, Lloyd KG. Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems. PLoS One 2023; 18:e0281277. [PMID: 37594978 PMCID: PMC10437873 DOI: 10.1371/journal.pone.0281277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/30/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.
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Affiliation(s)
- Raegan Paul
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Timothy J. Rogers
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Kate M. Fullerton
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Murray H. Stokes
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Andrew D. Steen
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - J. Maarten de Moor
- Observatorio Volcanológico y Sismológico de Costa Rica (OVSICORI) Universidad Nacional, Heredia, Costa Rica
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, United States of America
| | - Agostina Chiodi
- Instituto de Bio y Geociencias del NOA (IBIGEO, UNSa-CONICET), Salta, Argentina
| | - Andri Stefánsson
- NordVulk, Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | - Gerdhard L. Jessen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Peter H. Barry
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- National Research Council–Institute of Marine Biological Resources and Biotechnologies—CNR-IRBIM, Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States of America
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
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6
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Bender AN, Krause DJ, Goebel ME, Hoffman JI, Lewallen EA, Bonin CA. Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator. PLoS One 2023; 18:e0284640. [PMID: 37566609 PMCID: PMC10420386 DOI: 10.1371/journal.pone.0284640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023] Open
Abstract
Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems. Ninety leopard seals were sampled from the northern Antarctic Peninsula during the austral summers of 2008-2019 and a 405bp segment of the mitochondrial control region was sequenced for each individual. We uncovered moderate levels of nucleotide (π = 0.013) and haplotype (Hd = 0.96) diversity, and the effective population size was estimated at around 24,000 individuals (NE = 24,376; 95% CI: 16,876-33,126). Consistent with findings from other ice-breeding pinnipeds, Bayesian skyline analysis also revealed evidence for population expansion during the last glacial maximum, suggesting that historical population growth may have been boosted by an increase in the abundance of sea ice. Although leopard seals can be found in warmer, sub-Antarctic locations, the species' core habitat is centered on the Antarctic, making it inherently vulnerable to the loss of sea ice habitat due to climate change. Therefore, detailed assessments of past and present leopard seal population trends are needed to inform policies for Antarctic ecosystems.
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Affiliation(s)
- Arona N. Bender
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
| | - Douglas J. Krause
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, United States of America
| | - Michael E. Goebel
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- British Antarctic Survey, Cambridge, United Kingdom
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
| | - Carolina A. Bonin
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
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7
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Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
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8
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Cooper KM, Anderson K, Cashman K, Coombs M, Dietterich H, Fischer T, Houghton B, Johanson I, Lynn KJ, Manga M, Wauthier C. Coordinating science during an eruption: lessons from the 2020-2021 Kīlauea volcanic eruption. Bull Volcanol 2023; 85:29. [PMID: 37090041 PMCID: PMC10102681 DOI: 10.1007/s00445-023-01644-1] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Data collected during well-observed eruptions can lead to dramatic increases in our understanding of volcanic processes. However, the necessary prioritization of public safety and hazard mitigation during a crisis means that scientific opportunities may be sacrificed. Thus, maximizing the scientific gains from eruptions requires improved planning and coordinating science activities among governmental organizations and academia before and during volcanic eruptions. One tool to facilitate this coordination is a Scientific Advisory Committee (SAC). In the USA, the Community Network for Volcanic Eruption Response (CONVERSE) has been developing and testing this concept during workshops and scenario-based activities. The December 2020 eruption of Kīlauea volcano, Hawaii, provided an opportunity to test and refine this model in real-time and in a real-world setting. We present here the working model of a SAC developed during this eruption. Successes of the Kīlauea SAC (K-SAC) included broadening the pool of scientists involved in eruption response and developing and codifying procedures that may form the basis of operation for future SACs. Challenges encountered by the K-SAC included a process of review and facilitation of research proposals that was too slow to include outside participation in the early parts of the eruption and a decision process that fell on a small number of individuals at the responding volcano observatory. Possible ways to address these challenges include (1) supporting community-building activities between eruptions that make connections among scientists within and outside formal observatories, (2) identifying key science questions and pre-planning science activities, which would facilitate more rapid implementation across a broader scientific group, and (3) continued dialog among observatory scientists, emergency responders, and non-observatory scientists about the role of SACs. The SAC model holds promise to become an integral part of future efforts, leading in the short and longer term to more effective hazard response and greater scientific discovery and understanding.
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Affiliation(s)
- Kari M. Cooper
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
| | - Kyle Anderson
- U.S. Geological Survey California Volcano Observatory, Moffett Field, CA 94035 USA
| | - Kathy Cashman
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403-1272 USA
| | - Michelle Coombs
- U.S. Geological Survey Alaska Volcano Observatory, Anchorage, AK 99508 USA
| | - Hannah Dietterich
- U.S. Geological Survey Alaska Volcano Observatory, Anchorage, AK 99508 USA
| | - Tobias Fischer
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131 USA
| | - Bruce Houghton
- Department of Earth Sciences, University of Hawai‘I, Honolulu, HI 96822 USA
| | - Ingrid Johanson
- U.S. Geological Survey Hawaiian Volcano Observatory, Hilo, HI 96720 USA
| | - Kendra J. Lynn
- U.S. Geological Survey Hawaiian Volcano Observatory, Hilo, HI 96720 USA
| | - Michael Manga
- Department of Earth and Planetary Science, University of California, Berkeley, McCone Hall, Berkeley, CA 94720 USA
| | - Christelle Wauthier
- Department of Geosciences, The Pennsylvania State University, State College, PA 16801 USA
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9
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Islam MR, Li T, Mahata K, Khanal N, Werden B, Giordano MR, Praveen Puppala S, Dhital NB, Gurung A, Saikawa E, Panday AK, Yokelson RJ, DeCarlo PF, Stone EA. Wintertime Air Quality across the Kathmandu Valley, Nepal: Concentration, Composition, and Sources of Fine and Coarse Particulate Matter. ACS Earth Space Chem 2022; 6:2955-2971. [PMID: 36561192 PMCID: PMC9761783 DOI: 10.1021/acsearthspacechem.2c00243] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
The Kathmandu Valley in Nepal experiences poor air quality, especially in the dry winter season. In this study, we investigated the concentration, chemical composition, and sources of fine and coarse particulate matter (PM2.5, PM10, and PM10-2.5) at three sites within or near the Kathmandu Valley during the winter of 2018 as part of the second Nepal Ambient Monitoring and Source Testing Experiment (NAMaSTE 2). Daily PM2.5 concentrations were very high throughout the study period, ranging 72-149 μg m-3 at the urban Ratnapark site in Kathmandu, 88-161 μg m-3 at the suburban Lalitpur site, and 40-74 μg m-3 at rural Dhulikhel on the eastern rim of the Kathmandu Valley. Meanwhile, PM10 ranged 194-309, 174-377, and 64-131 μg m-3, respectively. At the Ratnapark site, crustal materials from resuspended soil contributed an average of 11% of PM2.5 and 34% of PM10. PM2.5 was largely comprised of organic carbon (OC, 28-30% by mass) and elemental carbon (EC, 10-14% by mass). As determined by chemical mass balance source apportionment modeling, major PM2.5 OC sources were garbage burning (15-21%), biomass burning (10-17%), and fossil fuel (14-26%). Secondary organic aerosol (SOA) contributions from aromatic volatile organic compounds (13-23% OC) were larger than those from isoprene (0.3-0.5%), monoterpenes (0.9-1.4%), and sesquiterpenes (3.6-4.4%). Nitro-monoaromatic compounds-of interest due to their light-absorbing properties and toxicity-indicate the presence of biomass burning-derived SOA. Knowledge of primary and secondary PM sources can facilitate air quality management in this region.
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Affiliation(s)
- Md. Robiul Islam
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Tianyi Li
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | | | - Benjamin Werden
- Department
of Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Michael R. Giordano
- Univ
Paris Est Creteil and Université de Paris, CNRS, LISA, Créteil 94000, France
| | - Siva Praveen Puppala
- International
Centre for Integrated Mountain Development (ICIMOD), Khumaltar, Lalitpur 44700, Nepal
| | - Narayan Babu Dhital
- Patan
Multiple
Campus, Department of Environmental Science, Tribhuvan University, Lalitpur 44700, Nepal
| | - Anobha Gurung
- Clean
Cooking Alliance, Washington, District of Columbia 20006, United States
| | - Eri Saikawa
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
| | - Arnico K. Panday
- Institute
for Integrated Development Studies (IIDS), Kathmandu 44600, Nepal
| | - Robert J. Yokelson
- Department
of Chemistry, University of Montana, Missoula, Montana 59812, United States
| | - Peter F. DeCarlo
- Department
of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Elizabeth. A. Stone
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
- Department
of Chemical and Biochemical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
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10
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Lyu F, Wang S, Han SY, Catlett C, Wang S. An integrated cyberGIS and machine learning framework for fine-scale prediction of Urban Heat Island using satellite remote sensing and urban sensor network data. Urban Inform 2022; 1:6. [PMID: 37522136 PMCID: PMC9458483 DOI: 10.1007/s44212-022-00002-4] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/01/2022] [Accepted: 06/22/2022] [Indexed: 11/29/2022]
Abstract
Due to climate change and rapid urbanization, Urban Heat Island (UHI), featuring significantly higher temperature in metropolitan areas than surrounding areas, has caused negative impacts on urban communities. Temporal granularity is often limited in UHI studies based on satellite remote sensing data that typically has multi-day frequency coverage of a particular urban area. This low temporal frequency has restricted the development of models for predicting UHI. To resolve this limitation, this study has developed a cyber-based geographic information science and systems (cyberGIS) framework encompassing multiple machine learning models for predicting UHI with high-frequency urban sensor network data combined with remote sensing data focused on Chicago, Illinois, from 2018 to 2020. Enabled by rapid advances in urban sensor network technologies and high-performance computing, this framework is designed to predict UHI in Chicago with fine spatiotemporal granularity based on environmental data collected with the Array of Things (AoT) urban sensor network and Landsat-8 remote sensing imagery. Our computational experiments revealed that a random forest regression (RFR) model outperforms other models with the prediction accuracy of 0.45 degree Celsius in 2020 and 0.8 degree Celsius in 2018 and 2019 with mean absolute error as the evaluation metric. Humidity, distance to geographic center, and PM2.5 concentration are identified as important factors contributing to the model performance. Furthermore, we estimate UHI in Chicago with 10-min temporal frequency and 1-km spatial resolution on the hottest day in 2018. It is demonstrated that the RFR model can accurately predict UHI at fine spatiotemporal scales with high-frequency urban sensor network data integrated with satellite remote sensing data.
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Affiliation(s)
- Fangzheng Lyu
- cyberGIS Center for Advanced Digital and Spatial Studies, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Geography and Geographic Information Science, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Shaohua Wang
- Key Laboratory of Digital Earth Science, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094 China
- International Research Center of Big Data for Sustainable Development Goals, Beijing, 100094 China
| | - Su Yeon Han
- cyberGIS Center for Advanced Digital and Spatial Studies, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Geography and Geographic Information Science, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Charlie Catlett
- Computing, Environment, and Life Sciences, Argonne National Laboratory, Chicago, IL USA
| | - Shaowen Wang
- cyberGIS Center for Advanced Digital and Spatial Studies, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Geography and Geographic Information Science, University of Illinois at Urbana-Champaign, Urbana, IL USA
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11
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Srikrishnan V, Guan Y, Tol RSJ, Keller K. Probabilistic projections of baseline twenty-first century CO 2 emissions using a simple calibrated integrated assessment model. Clim Change 2022; 170:37. [PMID: 35228765 PMCID: PMC8866549 DOI: 10.1007/s10584-021-03279-7] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Probabilistic projections of baseline (with no additional mitigation policies) future carbon emissions are important for sound climate risk assessments. Deep uncertainty surrounds many drivers of projected emissions. Here, we use a simple integrated assessment model, calibrated to century-scale data and expert assessments of baseline emissions, global economic growth, and population growth, to make probabilistic projections of carbon emissions through 2100. Under a variety of assumptions about fossil fuel resource levels and decarbonization rates, our projections largely agree with several emissions projections under current policy conditions. Our global sensitivity analysis identifies several key economic drivers of uncertainty in future emissions and shows important higher-level interactions between economic and technological parameters, while population uncertainties are less important. Our analysis also projects relatively low global economic growth rates over the remainder of the century. This illustrates the importance of additional research into economic growth dynamics for climate risk assessment, especially if pledged and future climate mitigation policies are weakened or have delayed implementations. These results showcase the power of using a simple, transparent, and calibrated model. While the simple model structure has several advantages, it also creates caveats for our results which are related to important areas for further research. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10584-021-03279-7.
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Affiliation(s)
- Vivek Srikrishnan
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY USA
| | - Yawen Guan
- Department of Statistics, University of Nebraska, Lincoln, NE USA
| | - Richard S. J. Tol
- Department of Economics, University of Sussex, Sussex, UK
- Institute for Environmental Studies, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Spatial Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Klaus Keller
- Department of Geosciences, Pennsylvania State University, University Park, PA USA
- Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
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12
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Turner KJ, Burls NJ, von Brandis A, Lübbecke J, Claus M. Seasonality in the relationship between equatorial-mean heat content and interannual eastern equatorial Atlantic sea surface temperature variability. Clim Dyn 2022; 59:61-75. [PMID: 35755453 PMCID: PMC9213350 DOI: 10.1007/s00382-021-06116-w] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
Interannual sea surface temperature (SST) variations in the tropical Atlantic Ocean lead to anomalous atmospheric circulation and precipitation patterns with important ecological and socioeconomic consequences for the semiarid regions of sub-Saharan Africa and northeast Brazil. This interannual SST variability is characterized by three modes: an Atlantic meridional mode featuring an anomalous cross-equatorial SST gradient that peaks in boreal spring; an Atlantic zonal mode (Atlantic Niño mode) with SST anomalies in the eastern equatorial Atlantic cold tongue region that peaks in boreal summer; and a second zonal mode of variability with eastern equatorial SST anomalies peaking in boreal winter. Here we investigate the extent to which there is any seasonality in the relationship between equatorial warm water recharge and the development of eastern equatorial Atlantic SST anomalies. Seasonally stratified cross-correlation analysis between eastern equatorial Atlantic SST anomalies and equatorial heat content anomalies (evaluated using warm water volume and sea surface height) indicate that while equatorial heat content changes do occasionally play a role in the development of boreal summer Atlantic zonal mode events, they contribute more consistently to Atlantic Niño II, boreal winter events. Event and composite analysis of ocean adjustment with a shallow water model suggest that the warm water volume anomalies originate mainly from the off-equatorial northwestern Atlantic, in agreement with previous studies linking them to anomalous wind stress curl associated with the Atlantic meridional mode.
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Affiliation(s)
- Kyle J. Turner
- Department of Atmospheric, Oceanic, and Earth Sciences, Center for Ocean-Land-Atmosphere Studies, George Mason University, 4400 University Drive, Fairfax, VA 22030 USA
| | - Natalie J. Burls
- Department of Atmospheric, Oceanic, and Earth Sciences, Center for Ocean-Land-Atmosphere Studies, George Mason University, 4400 University Drive, Fairfax, VA 22030 USA
| | - Anna von Brandis
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Christian-Albrechts-Universität zu Kiel (CAU), Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Joke Lübbecke
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Christian-Albrechts-Universität zu Kiel (CAU), Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Martin Claus
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Christian-Albrechts-Universität zu Kiel (CAU), Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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13
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Yu JR, LeRoy G, Bready D, Frenster JD, Saldaña-Meyer R, Jin Y, Descostes N, Stafford JM, Placantonakis DG, Reinberg D. The H3K36me2 writer-reader dependency in H3K27M-DIPG. Sci Adv 2021; 7:eabg7444. [PMID: 34261657 PMCID: PMC8279504 DOI: 10.1126/sciadv.abg7444] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/01/2021] [Indexed: 05/12/2023]
Abstract
Histone H3K27M is a driving mutation in diffuse intrinsic pontine glioma (DIPG), a deadly pediatric brain tumor. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity and displacement of H3K27me2/3, promoting oncogenesis of DIPG. As a consequence, a histone modification H3K36me2, antagonistic to H3K27me2/3, is aberrantly elevated. Here, we investigate the role of H3K36me2 in H3K27M-DIPG by tackling its upstream catalyzing enzymes (writers) and downstream binding factors (readers). We determine that NSD1 and NSD2 are the key writers for H3K36me2. Loss of NSD1/2 in H3K27M-DIPG impedes cellular proliferation and tumorigenesis by disrupting tumor-promoting transcriptional programs. Further, we demonstrate that LEDGF and HDGF2 are the main readers mediating the protumorigenic effects downstream of NSD1/2-H3K36me2. Treatment with a chemically modified peptide mimicking endogenous H3K36me2 dislodges LEDGF/HDGF2 from chromatin and specifically inhibits the proliferation of H3K27M-DIPG. Our results indicate a functional pathway of NSD1/2-H3K36me2-LEDGF/HDGF2 as an acquired dependency in H3K27M-DIPG.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Devin Bready
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Joshua D Frenster
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Ying Jin
- Shared Bioinformatics Core Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
- EMBL Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
- Department of Neurological Sciences, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Stem Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
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14
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Stachelek J, Weng W, Carey CC, Kemanian AR, Cobourn KM, Wagner T, Weathers KC, Soranno PA. Granular measures of agricultural land use influence lake nitrogen and phosphorus differently at macroscales. Ecol Appl 2020; 30:e02187. [PMID: 32485044 DOI: 10.1002/eap.2187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Agricultural land use is typically associated with high stream nutrient concentrations and increased nutrient loading to lakes. For lakes, evidence for these associations mostly comes from studies on individual lakes or watersheds that relate concentrations of nitrogen (N) or phosphorus (P) to aggregate measures of agricultural land use, such as the proportion of land used for agriculture in a lake's watershed. However, at macroscales (i.e., in hundreds to thousands of lakes across large spatial extents), there is high variability around such relationships and it is unclear whether considering more granular (or detailed) agricultural data, such as fertilizer application, planting of specific crops, or the extent of near-stream cropping, would improve prediction and inform understanding of lake nutrient drivers. Furthermore, it is unclear whether lake N and P would have different relationships to such measures and whether these relationships would vary by region, since regional variation has been observed in prior studies using aggregate measures of agriculture. To address these knowledge gaps, we examined relationships between granular measures of agricultural activity and lake total phosphorus (TP) and total nitrogen (TN) concentrations in 928 lakes and their watersheds in the Northeastern and Midwest U.S. using a Bayesian hierarchical modeling approach. We found that both lake TN and TP concentrations were related to these measures of agriculture, especially near-stream agriculture. The relationships between measures of agriculture and lake TN concentrations were more regionally variable than those for TP. Conversely, TP concentrations were more strongly related to lake-specific measures like depth and watershed hydrology relative to TN. Our finding that lake TN and TP concentrations have different relationships with granular measures of agricultural activity has implications for the design of effective and efficient policy approaches to maintain and improve water quality.
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Affiliation(s)
- Joseph Stachelek
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| | - W Weng
- School of Business, State University of New York College at Geneseo, 1 College Circle, Geneseo, New York, 14454, USA
| | - C C Carey
- Department of Biological Sciences, Virginia Tech, 926 W Campus Drive, Blacksburg, Virginia, 24061, USA
| | - A R Kemanian
- Department of Plant Science, The Pennsylvania State University, 247 Agricultural Sciences and Industries Bldg., University Park, Pennsylvania, 16802, USA
| | - K M Cobourn
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 W Campus Drive, Blacksburg, Virginia, 24061, USA
| | - T Wagner
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - K C Weathers
- Cary Institute of Ecosystem Studies, 2801 Sharon Turnpike, Millbrook, New York, 12545, USA
| | - P A Soranno
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
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15
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Whalen KE, Becker JW, Schrecengost AM, Gao Y, Giannetti N, Harvey EL. Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean. Microbiome 2019; 7:93. [PMID: 31208456 PMCID: PMC6580654 DOI: 10.1186/s40168-019-0711-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/05/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Marine bacteria form complex relationships with eukaryotic hosts, from obligate symbioses to pathogenic interactions. These interactions can be tightly regulated by bioactive molecules, creating a complex system of chemical interactions through which these species chemically communicate thereby directly altering the host's physiology and community composition. Quorum sensing (QS) signals were first described in a marine bacterium four decades ago, and since then, we have come to discover that QS mediates processes within the marine carbon cycle, affects the health of coral reef ecosystems, and shapes microbial diversity and bacteria-eukaryotic host relationships. Yet, only recently have alkylquinolone signals been recognized for their role in cell-to-cell communication and the orchestration of virulence in biomedically relevant pathogens. The alkylquinolone, 2-heptyl-4-quinolone (HHQ), was recently found to arrest cell growth without inducing cell mortality in selected phytoplankton species at nanomolar concentrations, suggesting QS molecules like HHQ can influence algal physiology, playing pivotal roles in structuring larger ecological frameworks. RESULTS To understand how natural communities of phytoplankton and bacteria respond to HHQ, field-based incubation experiments with ecologically relevant concentrations of HHQ were conducted over the course of a stimulated phytoplankton bloom. Bulk flow cytometry measurements indicated that, in general, exposure to HHQ caused nanoplankton and prokaryotic cell abundances to decrease. Amplicon sequencing revealed HHQ exposure altered the composition of particle-associated and free-living microbiota, favoring the relative expansion of both gamma- and alpha-proteobacteria, and a concurrent decrease in Bacteroidetes. Specifically, Pseudoalteromonas spp., known to produce HHQ, increased in relative abundance following HHQ exposure. A search of representative bacterial genomes from genera that increased in relative abundance when exposed to HHQ revealed that they all have the genetic potential to bind HHQ. CONCLUSIONS This work demonstrates HHQ has the capacity to influence microbial community organization, suggesting alkylquinolones have functions beyond bacterial communication and are pivotal in driving microbial community structure and phytoplankton growth. Knowledge of how bacterial signals alter marine communities will serve to deepen our understanding of the impact these chemical interactions have on a global scale.
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Affiliation(s)
| | - Jamie W Becker
- Department of Biology, Haverford College, Haverford, PA, USA.
| | | | - Yongjie Gao
- Department of Biology, Haverford College, Haverford, PA, USA
| | | | - Elizabeth L Harvey
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
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16
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Lemkau KL, Reddy CM, Carmichael CA, Aeppli C, Swarthout RF, White HK. Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. PLoS One 2019; 14:e0213464. [PMID: 30883566 PMCID: PMC6422254 DOI: 10.1371/journal.pone.0213464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/25/2018] [Accepted: 02/21/2019] [Indexed: 11/18/2022] Open
Abstract
Prior to Hurricane Isaac making landfall along the Gulf of Mexico coast in August 2012, local and state officials were concerned that the hurricane would mobilize submerged oiled-materials from the Deepwater Horizon (DWH) spill. In this study, we investigated materials washed ashore following the hurricane to determine if it affected the chemical composition or density of oil-containing sand patties regularly found on Gulf Coast beaches. While small changes in sand patty density were observed in samples collected before and after the hurricane, these variations appear to have been driven by differences in sampling location and not linked to the passing of Hurricane Isaac. Visual and chemical analysis of sand patties confirmed that the contents was consistent with oil from the Macondo well. Petroleum hydrocarbon signatures of samples collected before and after the hurricane showed no notable changes. In the days following Hurricane Isaac, dark-colored mats were also found on the beach in Fort Morgan, AL, and community reports speculated that these mats contained oil from the DWH spill. Chemical analysis of these mat samples identified n-alkanes but no other petroleum hydrocarbons. Bulk and δ13C organic carbon analyses indicated mat samples were comprised of marshland peat and not related to the DWH spill. This research indicates that Hurricane Isaac did not result in a notable change the composition of oil delivered to beaches at the investigated field sites. This study underscores the need for improved communications with interested stakeholders regarding how to differentiate oiled from non-oiled materials. This is especially important given the high cost of removing oiled debris and the increasing likelihood of false positives as oiled-materials washing ashore from a spill become less abundant over time.
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Affiliation(s)
- Karin L. Lemkau
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
- * E-mail:
| | - Christopher M. Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Catherine A. Carmichael
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Christoph Aeppli
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Robert F. Swarthout
- Department of Chemistry and Environmental Science Program, Appalachian State University, Boone, North Carolina, United States of America
| | - Helen K. White
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, United States of America
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17
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Stettz S, Zaitchik BF, Ademe D, Musie S, Simane B. Estimating variability in downwelling surface shortwave radiation in a tropical highland environment. PLoS One 2019; 14:e0211220. [PMID: 30802255 PMCID: PMC6394370 DOI: 10.1371/journal.pone.0211220] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/09/2019] [Indexed: 11/25/2022] Open
Abstract
Surface incoming shortwave (solar) radiation data are an important component of many scientific analyses, but direct measurements are not commonly available. Estimates can be obtained from gridded meteorological analysis or reanalysis systems, such as the Global Data Assimilation Systems (GDAS) and Modern Era Retrospective Reanalysis System (MERRA-2), or calculated using empirical models dependent on meteorological variables such as air temperature. The purpose of this analysis was to compare multiple methods for estimating daily shortwave radiation in a tropical highland environment in Ethiopia. Direct solar radiation outputs of GDAS and MERRA-2, topographically corrected outputs of the two analysis systems, and empirically estimated solar radiation values calculated with the systems' air temperature data were compared to see which produced the most reliable radiation values. GDAS appeared to underestimate the seasonal variability, resulting in low correlation (R2) with in situ data and large mean bias error (MBE). In comparison, MERRA-2 did not underestimate variability, but produced larger bias than the empirical model estimates. There was an improvement in correlation and reduction in MBE when using the GDAS air temperature predictions in the empirical model, but the opposite was true for MERRA-2. The empirical model using station air temperature data (stationT) produced the highest correlation across all four stations, with best performance at the lower elevation sites. The direct shortwave radiation outputs of MERRA-2 produced comparable correlation values, with larger R2 at stations at higher elevation. Topography possibly influenced these results, as MERRA-2 performed comparably to stationT at the stations in moderate terrain, but not in steeper terrain. This work can serve as a starting point for analyses in other tropical highland regions, where continuous in situ solar radiation data are rarely available.
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Affiliation(s)
- Stephanie Stettz
- Department of Earth & Planetary Sciences, Johns Hopkins University,
Baltimore, Maryland, United States of America
| | - Benjamin F. Zaitchik
- Department of Earth & Planetary Sciences, Johns Hopkins University,
Baltimore, Maryland, United States of America
| | - Dereje Ademe
- Debre Markos University, Debre Markos, Amhara, Ethiopia
| | | | - Belay Simane
- College of Development Studies, Addis Ababa University, Addis Ababa,
Ethiopia
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18
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Rooney-Varga JN, Sterman JD, Fracassi E, Franck T, Kapmeier F, Kurker V, Johnston E, Jones AP, Rath K. Combining role-play with interactive simulation to motivate informed climate action: Evidence from the World Climate simulation. PLoS One 2018; 13:e0202877. [PMID: 30161185 PMCID: PMC6117006 DOI: 10.1371/journal.pone.0202877] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 08/28/2017] [Accepted: 08/10/2018] [Indexed: 11/25/2022] Open
Abstract
Climate change communication efforts grounded in the information deficit model have largely failed to close the gap between scientific and public understanding of the risks posed by climate change. In response, simulations have been proposed to enable people to learn for themselves about this complex and politically charged topic. Here we assess the impact of a widely-used simulation, World Climate, which combines a socially and emotionally engaging role-play with interactive exploration of climate change science through the C-ROADS climate simulation model. Participants take on the roles of delegates to the UN climate negotiations and are challenged to create an agreement that meets international climate goals. Their decisions are entered into C-ROADS, which provides immediate feedback about expected global climate impacts, enabling them to learn about climate change while experiencing the social dynamics of negotiations. We assess the impact of World Climate by analyzing pre- and post-survey results from >2,000 participants in 39 sessions in eight nations. We find statistically significant gains in three areas: (i) knowledge of climate change causes, dynamics and impacts; (ii) affective engagement including greater feelings of urgency and hope; and (iii) a desire to learn and do more about climate change. Contrary to the deficit model, gains in urgency were associated with gains in participants’ desire to learn more and intent to act, while gains in climate knowledge were not. Gains were just as strong among American participants who oppose government regulation of free markets–a political ideology that has been linked to climate change denial in the US–suggesting the simulation’s potential to reach across political divides. The results indicate that World Climate offers a climate change communication tool that enables people to learn and feel for themselves, which together have the potential to motivate action informed by science.
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Affiliation(s)
- J. N. Rooney-Varga
- UMass Lowell Climate Change Initiative and Department of Environmental, Earth and Atmospheric Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, United States of America
- * E-mail:
| | - J. D. Sterman
- System Dynamics Group, MIT Sloan School of Management, Cambridge, Massachusetts, United States of America
| | - E. Fracassi
- Escuela de Ingeniería y Gestión, Instituto Tecnológico de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - T. Franck
- Climate Interactive, Washington, DC, United States of America
| | | | - V. Kurker
- UMass Lowell Climate Change Initiative and Department of Environmental, Earth and Atmospheric Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, United States of America
| | - E. Johnston
- Climate Interactive, Washington, DC, United States of America
| | - A. P. Jones
- Climate Interactive, Washington, DC, United States of America
| | - K. Rath
- SageFox Consulting Group, Amherst, Massachusetts, United States of America
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19
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Abstract
While one system is animate and the other inanimate, both plants and cars are powered by a highly successful process which has evolved in a changing environment. Each process (the photosynthetic pathway and the car engine, respectively) originated from a basic scheme and evolved greater efficiency by adding components to the existing structure, which has remained largely unchanged. Here we present a comparative analysis of two variants on the original C3 photosynthetic pathway (C4 and CAM) and two variants on the internal combustion engine (the turbocharger and the hybrid electric vehicle). We compare the timeline of evolution, the interaction between system components, and the effects of environmental conditions on both systems. This analysis reveals striking similarities in the development of these processes, providing insight as to how complex systems—both natural and built—evolve and adapt to changing environmental conditions in a modular fashion.
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Affiliation(s)
- Samantha Hartzell
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, United States of America
- Princeton Environmental Institute, Princeton University, Princeton, NJ, United States of America
| | - Mark Bartlett
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, United States of America
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Jun Yin
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, United States of America
- Princeton Environmental Institute, Princeton University, Princeton, NJ, United States of America
| | - Amilcare Porporato
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, United States of America
- Princeton Environmental Institute, Princeton University, Princeton, NJ, United States of America
- * E-mail:
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20
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Abstract
Organisms may energetically finance reproductive effort using energy stored prior to the reproductive period (termed capital breeders) or using energy acquired during the reproductive period (termed income breeders). The specific strategy used has implications for population dynamics as well as for the response to environmental variation. Crabs and other crustaceans have generally been assumed to be capital breeders. Here I demonstrate an experimental procedure used to determine whether crabs are capable of using an income breeding strategy. I then examine data from several published studies from a range of crab species across a broad phylogenetic spectrum that conducted similar experiments to look for evidence of income breeding strategy. I show that income breeding does occur in crabs, but that it appears to be taxon-specific. In particular, I show that income breeding occurs in two species from the family Portunidae, but fail to find evidence for income breeding in other taxa examined. This finding has a range of implications for this ecologically and economically important group of consumers, including implications for their response to human-induced environmental change, their response to fishing pressure, and best practices for aquaculture. The implications of breeding strategy in crabs likely depends on phylogeny (morphology) and ecology, both of which influence the space available for energy storage inside the carapace.
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Affiliation(s)
- Blaine D. Griffen
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
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21
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Stukel MR, Décima M, Kelly TB. A new approach for incorporating 15N isotopic data into linear inverse ecosystem models with Markov Chain Monte Carlo sampling. PLoS One 2018; 13:e0199123. [PMID: 29912928 PMCID: PMC6005467 DOI: 10.1371/journal.pone.0199123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 01/30/2018] [Accepted: 06/03/2018] [Indexed: 11/23/2022] Open
Abstract
Oceanographic field programs often use δ15N biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating δ15N isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this approach to recover food web indices (nitrate uptake, nitrogen fixation, zooplankton trophic level, and secondary production) derived from forward models simulating the planktonic ecosystems of the California Current and Amazon River Plume. We show that the MCMC with δ15N approach typically does a better job of recovering ecosystem structure than the standard MCMC or L2 minimum norm (L2MN) approaches, and also outperforms an L2MN with δ15N approach. Furthermore, we find that the MCMC with δ15N approach is robust to the removal of input equations and hence is well suited to typical pelagic ecosystem studies for which the system is usually vastly under-constrained. Our approach is easily extendable for use with δ13C isotopic measurements or variable carbon:nitrogen stoichiometry.
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Affiliation(s)
- Michael R. Stukel
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, United States of America
- Center for Ocean-Atmospheric Prediction Studies, Florida State University, Tallahassee, FL, United States of America
- * E-mail:
| | - Moira Décima
- National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand
| | - Thomas B. Kelly
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, United States of America
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Lyons LR, Zou Y, Nishimura Y, Gallardo-Lacourt B, Angelopulos V, Donovan EF. Stormtime substorm onsets: occurrence and flow channel triggering. Earth Planets Space 2018; 70:81. [PMID: 31258379 PMCID: PMC6560977 DOI: 10.1186/s40623-018-0857-x] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/07/2018] [Indexed: 06/09/2023]
Abstract
Bright auroral emissions during geomagnetic storms provide a good opportunity for testing the proposal that substorm onset is frequently triggered by plasma sheet flow bursts that are manifested in the ionosphere as auroral streamers. We have used the broad coverage of the ionospheric mapping of the plasma sheet offered by the high-resolution THEMIS all-sky-imagers (ASIs) and chose the main phases of 9 coronal mass ejection (CME) related and 9 high-speed stream (HSS)-related geomagnetic storms, and identified substorm auroral onsets defined as brightening followed by poleward expansion. We found a detectable streamer heading to near the substorm onset location for all 60 onsets that we identified and were observed well by the ASIs. This indicates that substorm onsets are very often triggered by the intrusion of plasma with lower entropy than the surrounding plasma to the onset region, with the caveat that the ASIs do not give a direct measure of the intruding plasma. The majority of the triggering streamers are "tilted streamers," which extend eastward as their eastern tip tilts equatorward to near the substorm onset location. Fourteen of the 60 cases were identified as "Harang streamers," where the streamer discernibly turns toward the west poleward of reaching to near the onset latitude, indicating flow around the Harang reversal. Using the ASI observations, we observed substantially less substorm onsets for CME storms than for HSS storms, a result in disagreement with a recent finding of approximately equal substorm occurrences. We suggest that this difference is a result of strong non-substorm streamers that give substorm-like signatures in ground magnetic field observations but are not substorms based on their auroral signature. Our results from CME storms with steady, strong southward IMF are not consistent with the ~ 2-4 h repetition of substorms that has been suggested for moderate to strong southward IMF conditions. Instead, our results indicate substantially lower substorm occurrence during such steady driving conditions. Our results also show the much more frequent occurrence of substorms during HSS period, which is likely due to the highly fluctuating IMF.
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Affiliation(s)
- Larry R. Lyons
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095-1565 USA
| | - Ying Zou
- Center for Space Physics and Department of Astronomy, Boston University, Boston, MA 02215 USA
- Cooperative Programs for the Advancement of Earth System Science, University Corporation for Atmospheric Research, Boulder, CO USA
| | - Yukitoshi Nishimura
- Center for Space Physics and Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215 USA
| | - Bea Gallardo-Lacourt
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive, Calgary, AB T2N 1N4 Canada
| | - Vassilis Angelopulos
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, CA 90095-1567 USA
| | - Eric F. Donovan
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive, Calgary, AB T2N 1N4 Canada
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23
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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Russell MP, Gibbs VK, Duwan E. Bioerosion by pit-forming, temperate-reef sea urchins: History, rates and broader implications. PLoS One 2018; 13:e0191278. [PMID: 29466357 PMCID: PMC5821313 DOI: 10.1371/journal.pone.0191278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 03/03/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022] Open
Abstract
Sea urchins are dominant members of rocky temperate reefs around the world. They often occur in cavities within the rock, and fit so tightly, it is natural to assume they sculpted these "pits." However, there are no experimental data demonstrating they bore pits. If they do, what are the rates and consequences of bioerosion to nearshore systems? We sampled purple sea urchins, Strongylocentrotus purpuratus, from sites with four rock types, three sedimentary (two sandstones and one mudstone) and one metamorphic (granite). A year-long experiment showed urchins excavated depressions on sedimentary rocks in just months. The rate of pit formation varied with rock type and ranged from <5 yr for medium-grain sandstone to >100 yr for granite. In the field, there were differences in pit size and shapes of the urchins (height:diameter ratio). The pits were shallow and urchins flatter at the granite site, and the pits were deeper and urchins taller at the sedimentary sites. Although overall pit sizes were larger on mudstone than on sandstone, urchin size accounted for this difference. A second, short-term experiment, showed the primary mechanism for bioerosion was ingestion of the substratum. This experiment eliminated potential confounding factors of the year-long experiment and yielded higher bioerosion rates. Given the high densities of urchins, large amounts of rock can be converted to sediment over short time periods. Urchins on sandstone can excavate as much as 11.4 kg m-2 yr-1. On a broader geographic scale, sediment production can exceed 100 t ha-1 yr-1, and across their range, their combined bioerosion is comparable to the sediment load of many rivers. The phase shift between urchin barrens and kelp bed habitats in the North Pacific is controlled by the trophic cascade of sea otters. By limiting urchin populations, these apex predators also may indirectly control a substantial component of coastal rates of bioerosion.
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Affiliation(s)
- Michael P. Russell
- Biology Department, Villanova University, Villanova, Pennsylvania, United States of America
- * E-mail:
| | - Victoria K. Gibbs
- Biology Department, Villanova University, Villanova, Pennsylvania, United States of America
| | - Emily Duwan
- Biology Department, Villanova University, Villanova, Pennsylvania, United States of America
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Carey R, Soule SA, Manga M, White JDL, McPhie J, Wysoczanski R, Jutzeler M, Tani K, Yoerger D, Fornari D, Caratori-Tontini F, Houghton B, Mitchell S, Ikegami F, Conway C, Murch A, Fauria K, Jones M, Cahalan R, McKenzie W. The largest deep-ocean silicic volcanic eruption of the past century. Sci Adv 2018; 4:e1701121. [PMID: 29326974 PMCID: PMC5762192 DOI: 10.1126/sciadv.1701121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
The 2012 submarine eruption of Havre volcano in the Kermadec arc, New Zealand, is the largest deep-ocean eruption in history and one of very few recorded submarine eruptions involving rhyolite magma. It was recognized from a gigantic 400-km2 pumice raft seen in satellite imagery, but the complexity of this event was concealed beneath the sea surface. Mapping, observations, and sampling by submersibles have provided an exceptionally high fidelity record of the seafloor products, which included lava sourced from 14 vents at water depths of 900 to 1220 m, and fragmental deposits including giant pumice clasts up to 9 m in diameter. Most (>75%) of the total erupted volume was partitioned into the pumice raft and transported far from the volcano. The geological record on submarine volcanic edifices in volcanic arcs does not faithfully archive eruption size or magma production.
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Affiliation(s)
- Rebecca Carey
- CODES and School of Physical Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - S. Adam Soule
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Michael Manga
- Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720–4767, USA
| | | | - Jocelyn McPhie
- CODES and School of Physical Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | - Martin Jutzeler
- CODES and School of Physical Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Kenichiro Tani
- Department of Geology and Paleontology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba-shi, Ibaraki 305-0005, Japan
| | - Dana Yoerger
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Daniel Fornari
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Bruce Houghton
- Geology and Geophysics, University of Hawaii at Manoa, 1680 East-West Road, Honolulu, HI 96825, USA
| | - Samuel Mitchell
- Geology and Geophysics, University of Hawaii at Manoa, 1680 East-West Road, Honolulu, HI 96825, USA
| | - Fumihiko Ikegami
- CODES and School of Physical Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Chris Conway
- Department of Geology and Paleontology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba-shi, Ibaraki 305-0005, Japan
| | - Arran Murch
- Geology Department, University of Otago, Dunedin 9054, New Zealand
| | - Kristen Fauria
- Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall, Berkeley, CA 94720–4767, USA
| | - Meghan Jones
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Woods Hole, MA 02543, USA
| | - Ryan Cahalan
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA
| | - Warren McKenzie
- Geology and Geophysics, University of Hawaii at Manoa, 1680 East-West Road, Honolulu, HI 96825, USA
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26
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Roncalli V, Christie AE, Sommer SA, Cieslak MC, Hartline DK, Lenz PH. A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health. PLoS One 2017; 12:e0186794. [PMID: 29065152 PMCID: PMC5655441 DOI: 10.1371/journal.pone.0186794] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 07/15/2017] [Accepted: 10/07/2017] [Indexed: 11/19/2022] Open
Abstract
Coral reef ecosystems of many sub-tropical and tropical marine coastal environments have suffered significant degradation from anthropogenic sources. Research to inform management strategies that mitigate stressors and promote a healthy ecosystem has focused on the ecology and physiology of coral reefs and associated organisms. Few studies focus on the surrounding pelagic communities, which are equally important to ecosystem function. Zooplankton, often dominated by small crustaceans such as copepods, is an important food source for invertebrates and fishes, especially larval fishes. The reef-associated zooplankton includes a sub-neustonic copepod family that could serve as an indicator species for the community. Here, we describe the generation of a de novo transcriptome for one such copepod, Labidocera madurae, a pontellid from an intensively-studied coral reef ecosystem, Kāne'ohe Bay, Oahu, Hawai'i. The transcriptome was assembled using high-throughput sequence data obtained from whole organisms. It comprised 211,002 unique transcripts, including 72,391 with coding regions. It was assessed for quality and completeness using multiple workflows. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified transcripts for 88% of expected eukaryotic core proteins. Targeted gene-discovery analyses included searches for transcripts coding full-length "giant" proteins (>4,000 amino acids), proteins and splice variants of voltage-gated sodium channels, and proteins involved in the circadian signaling pathway. Four different reference transcriptomes were generated and compared for the detection of differential gene expression between copepodites and adult females; 6,229 genes were consistently identified as differentially expressed between the two regardless of reference. Automated bioinformatics analyses and targeted manual gene curation suggest that the de novo assembled L. madurae transcriptome is of high quality and completeness. This transcriptome provides a new resource for assessing the global physiological status of a planktonic species inhabiting a coral reef ecosystem that is subjected to multiple anthropogenic stressors. The workflows provide a template for generating and assessing transcriptomes in other non-model species.
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Affiliation(s)
- Vittoria Roncalli
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
| | - Andrew E. Christie
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
| | - Stephanie A. Sommer
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
| | - Matthew C. Cieslak
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
| | - Daniel K. Hartline
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
| | - Petra H. Lenz
- Békésy Laboratory of Neurobiology, University of Hawai‘i at Mānoa, Honolulu, HI, United States of America
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27
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Abstract
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant litter diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation’s constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.
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Affiliation(s)
- Mia R. Maltz
- Center for Conservation Biology, University of California Riverside, Riverside, California, United States of America
- * E-mail:
| | - Kathleen K. Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Krista L. McGuire
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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28
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Kerkhof LJ, Dillon KP, Häggblom MM, McGuinness LR. Profiling bacterial communities by MinION sequencing of ribosomal operons. Microbiome 2017; 5:116. [PMID: 28911333 PMCID: PMC5599880 DOI: 10.1186/s40168-017-0336-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/30/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification. RESULTS To test the approach, bacterial rRNA operons (~ 4200 bp) were amplified from six DNA samples employing a mixture of farm soil and bioreactor DNA in known concentrations. Each DNA sample mixture was barcoded, sequenced in quadruplicate (n = 24), on two separate 6-h runs using the MinION system (R7.3 flow cell; MAP005 and 006 chemistry). From nearly 90,000 MinION reads, roughly 33,000 forward and reverse sequences were obtained. This yielded over 10,000 2D sequences which were analyzed using a simplified data analysis pipeline based on NCBI Blast and assembly with Geneious software. The method could detect over 1000 operational taxonomic units in the sample sets in a quantitative manner. Global sequence coverage for the various rRNA operons ranged from 1 to 1951x. An iterative assembly scheme was developed to reconstruct those rRNA operons with > 35x coverage from a set of 30 operational taxonomic units (OTUs) among the Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Gemmatimonadetes. Phylogenetic analysis of the 16S rRNA and 23S rRNA genes from each operon demonstrated similar tree topologies with species/strain-level resolution. CONCLUSIONS This sequencing method represents a cost-effective way to profile microbial communities. Because the MinION is small, portable, and runs on a laptop, the possibility of microbiota characterization in the field or on robotic platforms becomes realistic.
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Affiliation(s)
- Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ, 08901-8521, USA.
| | - Kevin P Dillon
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ, 08901-8521, USA
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29
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Arakawa N, Aluwihare LI, Simpson AJ, Soong R, Stephens BM, Lane-Coplen D. Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter. Sci Adv 2017; 3:e1602976. [PMID: 28959723 PMCID: PMC5617377 DOI: 10.1126/sciadv.1602976] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/06/2017] [Indexed: 05/31/2023]
Abstract
The ocean's biota sequester atmospheric carbon dioxide (CO2) in part by producing dissolved organic matter (DOM) that persists in the ocean for millennia. This long-term accumulation of carbon may be facilitated by abiotic and biotic production of chemical structures that resist degradation, consequently contributing disproportionately to refractory DOM. Compounds that are selectively preserved in seawater were identified in solid-phase extracted DOM (PPL-DOM) using comprehensive gas chromatography (GC) coupled to mass spectrometry (MS). These molecules contained cyclic head groups that were linked to isoprenoid tails, and their overall structures closely resembled carotenoid degradation products (CDP). The origin of these compounds in PPL-DOM was further confirmed with an in vitro β-carotene photooxidation experiment that generated water-soluble CDP with similar structural characteristics. The molecular-level identification linked at least 10% of PPL-DOM carbon, and thus 4% of total DOM carbon, to CDP. Nuclear magnetic resonance spectra of experimental CDP and environmental PPL-DOM overlapped considerably, which indicated that even a greater proportion of PPL-DOM was likely composed of CDP. The CDP-rich DOM fraction was depleted in radiocarbon (14C age > 1500 years), a finding that supports the possible long-term accumulation of CDP in seawater. By linking a specific class of widespread biochemicals to refractory DOM, this work provides a foundation for future studies that aim to examine how persistent DOM forms in the ocean.
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Affiliation(s)
- Neal Arakawa
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Andre J. Simpson
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
| | - Brandon M. Stephens
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0244, USA
| | - Daniel Lane-Coplen
- Environmental Nuclear Magnetic Resonance Center, University of Toronto, Scarborough Campus, Toronto, Ontario M1C 1A4, Canada
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Wang Y, Zhu L, Shi F, Schubnel A, Hilairet N, Yu T, Rivers M, Gasc J, Addad A, Deldicque D, Li Z, Brunet F. A laboratory nanoseismological study on deep-focus earthquake micromechanics. Sci Adv 2017; 3:e1601896. [PMID: 28776024 PMCID: PMC5521995 DOI: 10.1126/sciadv.1601896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 06/16/2017] [Indexed: 06/01/2023]
Abstract
Global earthquake occurring rate displays an exponential decay down to ~300 km and then peaks around 550 to 600 km before terminating abruptly near 700 km. How fractures initiate, nucleate, and propagate at these depths remains one of the greatest puzzles in earth science, as increasing pressure inhibits fracture propagation. We report nanoseismological analysis on high-resolution acoustic emission (AE) records obtained during ruptures triggered by partial transformation from olivine to spinel in Mg2GeO4, an analog to the dominant mineral (Mg,Fe)2SiO4 olivine in the upper mantle, using state-of-the-art seismological techniques, in the laboratory. AEs' focal mechanisms, as well as their distribution in both space and time during deformation, are carefully analyzed. Microstructure analysis shows that AEs are produced by the dynamic propagation of shear bands consisting of nanograined spinel. These nanoshear bands have a near constant thickness (~100 nm) but varying lengths and self-organize during deformation. This precursory seismic process leads to ultimate macroscopic failure of the samples. Several source parameters of AE events were extracted from the recorded waveforms, allowing close tracking of event initiation, clustering, and propagation throughout the deformation/transformation process. AEs follow the Gutenberg-Richter statistics with a well-defined b value of 1.5 over three orders of moment magnitudes, suggesting that laboratory failure processes are self-affine. The seismic relation between magnitude and rupture area correctly predicts AE magnitude at millimeter scales. A rupture propagation model based on strain localization theory is proposed. Future numerical analyses may help resolve scaling issues between laboratory AE events and deep-focus earthquakes.
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Affiliation(s)
- Yanbin Wang
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60439, USA
| | - Lupei Zhu
- Department of Earth and Atmospheric Sciences, St. Louis University, St. Louis, MO 63108, USA
| | - Feng Shi
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60439, USA
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences, Wuhan, China
| | - Alexandre Schubnel
- Laboratoire de Géologie, CNRS UMR 8538, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Nadege Hilairet
- Université de Lille, CNRS, INRA, ENSCL, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - Tony Yu
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60439, USA
| | - Mark Rivers
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60439, USA
| | - Julien Gasc
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60439, USA
| | - Ahmed Addad
- Université de Lille, CNRS, INRA, ENSCL, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - Damien Deldicque
- Laboratoire de Géologie, CNRS UMR 8538, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Ziyu Li
- Department of Earth and Atmospheric Sciences, St. Louis University, St. Louis, MO 63108, USA
| | - Fabrice Brunet
- Université Grenoble Alpes, CNRS, ISTerre, Grenoble, France
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Cresci A, Paris CB, Durif CMF, Shema S, Bjelland RM, Skiftesvik AB, Browman HI. Glass eels ( Anguilla anguilla) have a magnetic compass linked to the tidal cycle. Sci Adv 2017; 3:e1602007. [PMID: 28630895 PMCID: PMC5466372 DOI: 10.1126/sciadv.1602007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 05/11/2017] [Indexed: 05/25/2023]
Abstract
The European eel (Anguilla anguilla) has one of the longest migrations in the animal kingdom. It crosses the Atlantic Ocean twice during its life history, migrating between the spawning area in the Sargasso Sea and Europe, where it is widely distributed. The leptocephalus larvae drift with the Gulf Stream and other currents for more than a year and metamorphose into glass eels when they arrive on the continental shelf and move toward coastal areas. The mechanisms underlying glass eel orientation toward the coast and into freshwater systems are poorly known. However, anguillid eels, including the glass eel life stage, have a geomagnetic sense, suggesting the possibility that they use Earth's magnetic field to orient toward the coast. To test this hypothesis, we used a unique combination of laboratory tests and in situ behavioral observations conducted in a drifting circular arena. Most (98%) of the glass eels tested in the sea exhibited a preferred orientation that was related to the tidal cycle. Seventy-one percent of the same eels showed the same orientation during ebb tide when tested in the laboratory under a manipulated simulated magnetic field in the absence of any other cue. These results demonstrate that glass eels use a magnetic compass for orientation and suggest that this magnetic orientation system is linked to a circatidal rhythm.
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Affiliation(s)
- Alessandro Cresci
- Department of Ocean Sciences, Rosenstiel School of Marine & Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149–1098, USA
| | - Claire B. Paris
- Department of Ocean Sciences, Rosenstiel School of Marine & Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149–1098, USA
| | - Caroline M. F. Durif
- Institute of Marine Research, Marine Ecosystem Acoustics Research Group, Austevoll Research Station, Sauganeset 16, 5392 Storebø, Norway
| | - Steven Shema
- Grótti ehf., Grundarstíg 4, 101 Reykjavík, Iceland
| | - Reidun M. Bjelland
- Institute of Marine Research, Marine Ecosystem Acoustics Research Group, Austevoll Research Station, Sauganeset 16, 5392 Storebø, Norway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Marine Ecosystem Acoustics Research Group, Austevoll Research Station, Sauganeset 16, 5392 Storebø, Norway
| | - Howard I. Browman
- Institute of Marine Research, Marine Ecosystem Acoustics Research Group, Austevoll Research Station, Sauganeset 16, 5392 Storebø, Norway
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Abstract
A likely consequence of global warming will be the redistribution of Earth's rain belts, affecting water availability for many of Earth's inhabitants. We consider three ways in which planetary warming might influence the global distribution of precipitation. The first possibility is that rainfall in the tropics will increase and that the subtropics and mid-latitudes will become more arid. A second possibility is that Earth's thermal equator, around which the planet's rain belts and dry zones are organized, will migrate northward. This northward shift will be a consequence of the Northern Hemisphere, with its large continental area, warming faster than the Southern Hemisphere, with its large oceanic area. A third possibility is that both of these scenarios will play out simultaneously. We review paleoclimate evidence suggesting that (i) the middle latitudes were wetter during the last glacial maximum, (ii) a northward shift of the thermal equator attended the abrupt Bølling-Allerød climatic transition ~14.6 thousand years ago, and (iii) a southward shift occurred during the more recent Little Ice Age. We also inspect trends in seasonal surface heating between the hemispheres over the past several decades. From these clues, we predict that there will be a seasonally dependent response in rainfall patterns to global warming. During boreal summer, in which the rate of recent warming has been relatively uniform between the hemispheres, wet areas will get wetter and dry regions will become drier. During boreal winter, rain belts and drylands will expand northward in response to differential heating between the hemispheres.
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Affiliation(s)
- Aaron E. Putnam
- School of Earth and Climate Sciences and Climate Change Institute, 224 Bryand Global Sciences Center, University of Maine, Orono, ME 04469, USA
- Lamont-Doherty Earth Observatory of Columbia University, 61 Route 9W/PO Box 1000, Palisades, NY 10964, USA
| | - Wallace S. Broecker
- Lamont-Doherty Earth Observatory of Columbia University, 61 Route 9W/PO Box 1000, Palisades, NY 10964, USA
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Jaramillo C, Romero I, D’Apolito C, Bayona G, Duarte E, Louwye S, Escobar J, Luque J, Carrillo-Briceño JD, Zapata V, Mora A, Schouten S, Zavada M, Harrington G, Ortiz J, Wesselingh FP. Miocene flooding events of western Amazonia. Sci Adv 2017; 3:e1601693. [PMID: 28508052 PMCID: PMC5415333 DOI: 10.1126/sciadv.1601693] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/03/2017] [Indexed: 05/15/2023]
Abstract
There is a considerable controversy about whether western Amazonia was ever covered by marine waters during the Miocene [23 to 5 Ma (million years ago)]. We investigated the possible occurrence of Miocene marine incursions in the Llanos and Amazonas/Solimões basins, using sedimentological and palynological data from two sediment cores taken in eastern Colombia and northwestern Brazil together with seismic information. We observed two distinct marine intervals in the Llanos Basin, an early Miocene that lasted ~0.9 My (million years) (18.1 to 17.2 Ma) and a middle Miocene that lasted ~3.7 My (16.1 to 12.4 Ma). These two marine intervals are also seen in Amazonas/Solimões Basin (northwestern Amazonia) but were much shorter in duration, ~0.2 My (18.0 to 17.8 Ma) and ~0.4 My (14.1 to 13.7 Ma), respectively. Our results indicate that shallow marine waters covered the region at least twice during the Miocene, but the events were short-lived, rather than a continuous full-marine occupancy of Amazonian landscape over millions of years.
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Affiliation(s)
- Carlos Jaramillo
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama
- Corresponding author.
| | - Ingrid Romero
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corporación Geológica Ares, Calle 44A No. 53-96, Bogotá, Colombia
| | - Carlos D’Apolito
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama
- Corporación Geológica Ares, Calle 44A No. 53-96, Bogotá, Colombia
- University of Birmingham, Birmingham, U.K
| | - German Bayona
- Corporación Geológica Ares, Calle 44A No. 53-96, Bogotá, Colombia
| | - Edward Duarte
- Corporación Geológica Ares, Calle 44A No. 53-96, Bogotá, Colombia
| | - Stephen Louwye
- Department of Geology, University of Ghent, Ghent, Belgium
| | | | - Javier Luque
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Jorge D. Carrillo-Briceño
- Paleontological Institute and Museum, University of Zürich, Karl-Schmid-Strasse 4, Zürich 8006, Switzerland
| | | | | | - Stefan Schouten
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, 1790 AB, Den Burg, Texel, Netherlands
| | - Michael Zavada
- University of Texas of the Permian Basin, Odessa, TX 79762, USA
| | | | - John Ortiz
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Frank P. Wesselingh
- Naturalis Biodiversity Center, P.O. Box 9517, Darwinweg 2, 2300 RA Leiden, Netherlands
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Bradley AS, Swanson PK, Muller EEL, Bringel F, Caroll SM, Pearson A, Vuilleumier S, Marx CJ. Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment. PLoS One 2017; 12:e0173323. [PMID: 28319163 PMCID: PMC5358736 DOI: 10.1371/journal.pone.0173323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 11/25/2016] [Accepted: 02/17/2017] [Indexed: 01/27/2023] Open
Abstract
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane.
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Affiliation(s)
- Alexander S. Bradley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Earth and Planetary Sciences, Washington University in St Louis, St Louis, MO, United States of America
| | - Paige K. Swanson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Emilie E. L. Muller
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Sean M. Caroll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States of America
| | - Stéphane Vuilleumier
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States of America
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States of America
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Hellweger FL, van Sebille E, Calfee BC, Chandler JW, Zinser ER, Swan BK, Fredrick ND. The Role of Ocean Currents in the Temperature Selection of Plankton: Insights from an Individual-Based Model. PLoS One 2016; 11:e0167010. [PMID: 27907181 PMCID: PMC5131974 DOI: 10.1371/journal.pone.0167010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 08/23/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Biogeography studies that correlate the observed distribution of organisms to environmental variables are typically based on local conditions. However, in cases with substantial translocation, like planktonic organisms carried by ocean currents, selection may happen upstream and local environmental factors may not be representative of those that shaped the local population. Here we use an individual-based model of microbes in the global surface ocean to explore this effect for temperature. We simulate up to 25 million individual cells belonging to up to 50 species with different temperature optima. Microbes are moved around the globe based on a hydrodynamic model, and grow and die based on local temperature. We quantify the role of currents using the “advective temperature differential” metric, which is the optimum temperature of the most abundant species from the model with advection minus that from the model without advection. This differential depends on the location and can be up to 4°C. Poleward-flowing currents, like the Gulf Stream, generally experience cooling and the differential is positive. We apply our results to three global datasets. For observations of optimum growth temperature of phytoplankton, accounting for the effect of currents leads to a slightly better agreement with observations, but there is large variability and the improvement is not statistically significant. For observed Prochlorococcus ecotype ratios and metagenome nucleotide divergence, accounting for advection improves the correlation significantly, especially in areas with relatively strong poleward or equatorward currents.
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Affiliation(s)
- Ferdi L. Hellweger
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail:
| | - Erik van Sebille
- Grantham Institute & Department of Physics, Imperial College London, London, United Kingdom
- ARC Centre of Excellence for Climate System Science, Climate Change Research Centre, University of New South Wales, Sydney, Australia
| | - Benjamin C. Calfee
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jeremy W. Chandler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Erik R. Zinser
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brandon K. Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Neil D. Fredrick
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, United States of America
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Rowley DB, Forte AM, Rowan CJ, Glišović P, Moucha R, Grand SP, Simmons NA. Kinematics and dynamics of the East Pacific Rise linked to a stable, deep-mantle upwelling. Sci Adv 2016; 2:e1601107. [PMID: 28028535 PMCID: PMC5182052 DOI: 10.1126/sciadv.1601107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/21/2016] [Indexed: 05/29/2023]
Abstract
Earth's tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth's dominant MOR, has been characterized by limited ridge-perpendicular migration and persistent, asymmetric ridge accretion that are anomalous relative to other MORs. We reconstruct the subduction-related buoyancy fluxes of plates on either side of the EPR. The general expectation is that greater slab pull should correlate with faster plate motion and faster spreading at the EPR. Moreover, asymmetry in slab pull on either side of the EPR should correlate with either ridge migration or enhanced plate velocity in the direction of greater slab pull. Based on our analysis, none of the expected correlations are evident. This implies that other forces significantly contribute to EPR behavior. We explain these observations using mantle flow calculations based on globally integrated buoyancy distributions that require core-mantle boundary heat flux of up to 20 TW. The time-dependent mantle flow predictions yield a long-lived deep-seated upwelling that has its highest radial velocity under the EPR and is inferred to control its observed kinematics. The mantle-wide upwelling beneath the EPR drives horizontal components of asthenospheric flows beneath the plates that are similarly asymmetric but faster than the overlying surface plates, thereby contributing to plate motions through viscous tractions in the Pacific region.
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Affiliation(s)
- David B. Rowley
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
| | - Alessandro M. Forte
- GEOTOP, Université du Québec à Montréal, Montréal, Québec H3C 3P8, Canada
- Department of Geological Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Christopher J. Rowan
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
- Department of Geology, Kent State University, 221 McGilvrey Hall, Kent, OH 44242, USA
| | - Petar Glišović
- GEOTOP, Université du Québec à Montréal, Montréal, Québec H3C 3P8, Canada
| | - Robert Moucha
- Department of Earth Sciences, Syracuse University, Syracuse, NY 13244, USA
| | - Stephen P. Grand
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nathan A. Simmons
- Atmospheric, Earth, and Energy Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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Williams RH, McGee D, Kinsley CW, Ridley DA, Hu S, Fedorov A, Tal I, Murray RW, deMenocal PB. Glacial to Holocene changes in trans-Atlantic Saharan dust transport and dust-climate feedbacks. Sci Adv 2016; 2:e1600445. [PMID: 28138515 PMCID: PMC5262466 DOI: 10.1126/sciadv.1600445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/20/2016] [Indexed: 05/30/2023]
Abstract
Saharan mineral dust exported over the tropical North Atlantic is thought to have significant impacts on regional climate and ecosystems, but limited data exist documenting past changes in long-range dust transport. This data gap limits investigations of the role of Saharan dust in past climate change, in particular during the mid-Holocene, when climate models consistently underestimate the intensification of the West African monsoon documented by paleorecords. We present reconstructions of African dust deposition in sediments from the Bahamas and the tropical North Atlantic spanning the last 23,000 years. Both sites show early and mid-Holocene dust fluxes 40 to 50% lower than recent values and maximum dust fluxes during the deglaciation, demonstrating agreement with records from the northwest African margin. These quantitative estimates of trans-Atlantic dust transport offer important constraints on past changes in dust-related radiative and biogeochemical impacts. Using idealized climate model experiments to investigate the response to reductions in Saharan dust's radiative forcing over the tropical North Atlantic, we find that small (0.15°C) dust-related increases in regional sea surface temperatures are sufficient to cause significant northward shifts in the Atlantic Intertropical Convergence Zone, increased precipitation in the western Sahel and Sahara, and reductions in easterly and northeasterly winds over dust source regions. Our results suggest that the amplifying feedback of dust on sea surface temperatures and regional climate may be significant and that accurate simulation of dust's radiative effects is likely essential to improving model representations of past and future precipitation variations in North Africa.
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Affiliation(s)
- Ross H. Williams
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David McGee
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher W. Kinsley
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - David A. Ridley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shineng Hu
- Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA
| | - Alexey Fedorov
- Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA
| | - Irit Tal
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richard W. Murray
- Department of Earth and Environment, Boston University, Boston, MA 02215, USA
| | - Peter B. deMenocal
- Department of Earth and Environmental Sciences, Columbia University, New York, NY 10027, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
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Jeong JH, Resop JP, Mueller ND, Fleisher DH, Yun K, Butler EE, Timlin DJ, Shim KM, Gerber JS, Reddy VR, Kim SH. Random Forests for Global and Regional Crop Yield Predictions. PLoS One 2016; 11:e0156571. [PMID: 27257967 PMCID: PMC4892571 DOI: 10.1371/journal.pone.0156571] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [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: 06/03/2015] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Accurate predictions of crop yield are critical for developing effective agricultural and food policies at the regional and global scales. We evaluated a machine-learning method, Random Forests (RF), for its ability to predict crop yield responses to climate and biophysical variables at global and regional scales in wheat, maize, and potato in comparison with multiple linear regressions (MLR) serving as a benchmark. We used crop yield data from various sources and regions for model training and testing: 1) gridded global wheat grain yield, 2) maize grain yield from US counties over thirty years, and 3) potato tuber and maize silage yield from the northeastern seaboard region. RF was found highly capable of predicting crop yields and outperformed MLR benchmarks in all performance statistics that were compared. For example, the root mean square errors (RMSE) ranged between 6 and 14% of the average observed yield with RF models in all test cases whereas these values ranged from 14% to 49% for MLR models. Our results show that RF is an effective and versatile machine-learning method for crop yield predictions at regional and global scales for its high accuracy and precision, ease of use, and utility in data analysis. RF may result in a loss of accuracy when predicting the extreme ends or responses beyond the boundaries of the training data.
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Affiliation(s)
- Jig Han Jeong
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Box 354115, Seattle, WA 98195, United States of America
| | - Jonathan P. Resop
- Department of Geographical Sciences, University of Maryland, College Park, MD, United States of America
- Crop Systems and Global Change Laboratory, USDA-ARS, Beltsville, MD 20705, United States of America
| | - Nathaniel D. Mueller
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States of America
| | - David H. Fleisher
- Crop Systems and Global Change Laboratory, USDA-ARS, Beltsville, MD 20705, United States of America
| | - Kyungdahm Yun
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Box 354115, Seattle, WA 98195, United States of America
| | - Ethan E. Butler
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108, United States of America
| | - Dennis J. Timlin
- Crop Systems and Global Change Laboratory, USDA-ARS, Beltsville, MD 20705, United States of America
| | - Kyo-Moon Shim
- Climate Change & Agroecology Division, National Institute of Agricultural Science, RDA, Suwon, Korea
| | - James S. Gerber
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108, United States of America
| | - Vangimalla R. Reddy
- Crop Systems and Global Change Laboratory, USDA-ARS, Beltsville, MD 20705, United States of America
| | - Soo-Hyung Kim
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Box 354115, Seattle, WA 98195, United States of America
- * E-mail:
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Kohl WT, McClure TI, Miner BG. Decreased Temperature Facilitates Short-Term Sea Star Wasting Disease Survival in the Keystone Intertidal Sea Star Pisaster ochraceus. PLoS One 2016; 11:e0153670. [PMID: 27128673 PMCID: PMC4851418 DOI: 10.1371/journal.pone.0153670] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 12/16/2015] [Accepted: 04/01/2016] [Indexed: 11/18/2022] Open
Abstract
An extensive 2013 mass mortality event along the West Coast of North America due to Sea Star Wasting Disease (SSWD) has affected at least 20 species of sea stars. Among environmental factors potentially contributing to the timing of the current outbreak, increased coastal water temperatures are hypothesized to have contributed to previous and current outbreaks of SSWD. With a laboratory experiment, we tested whether cooler temperatures, similar to average winter temperatures, compared to average summer temperatures could slow the progression of morbidity or prevent SSWD mortality entirely in Pisaster ochraceus. Sea stars housed in cooler water progressed through SSWD states more slowly than sea stars housed at summer temperatures. However, the cooler temperature did not prevent SSWD mortality, and all stars died of the disease. Our data are consistent with experimental studies and field observations during previous and current outbreaks, and support the hypothesis that changes in coastal water temperatures have influenced one of the largest disease related mass mortality events in our oceans.
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Affiliation(s)
- Warren T. Kohl
- Western Washington University, 516 High Street, Bellingham, WA, 98225, United States of America
| | - Timothy I. McClure
- Western Washington University, 516 High Street, Bellingham, WA, 98225, United States of America
| | - Benjamin G. Miner
- Western Washington University, 516 High Street, Bellingham, WA, 98225, United States of America
- * E-mail:
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