Insights into the loss factors of phytoplankton blooms : the role of cell mortality in the decline of two inshore Alexandrium blooms

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 62 (2017): 1742–1753, doi:10.1002/lno.10530.While considerable effort has been devoted to understanding the factors regulating the development of phytoplankton blooms, the mechanisms leading to bloom decline and termination have received less attention. Grazing and sedimentation have been invoked as the main routes for the loss of phytoplankton biomass, and more recently, viral lysis, parasitism and programmed cell death (PCD) have been recognized as additional removal factors. Despite the importance of bloom declines to phytoplankton dynamics, the incidence and significance of various loss factors in regulating phytoplankton populations have not been widely characterized in natural blooms. To understand mechanisms controlling bloom decline, we studied two independent, inshore blooms of Alexandrium fundyense, paying special attention to cell mortality as a loss pathway. We observed increases in the number of dead cells with PCD features after the peak of both blooms, demonstrating a role for cell mortality in their terminations. In both blooms, sexual cyst formation appears to have been the dominant process leading to bloom termination, as both blooms were dominated by small-sized gamete cells near their peaks. Cell death and parasitism became more significant as sources of cell loss several days after the onset of bloom decline. Our findings show two distinct phases of bloom decline, characterized by sexual fusion as the initial dominant cell removal processes followed by elimination of remaining cells by cell death and parasitism.This article is a result of research funded by the National Oceanic and Atmospheric Administration Center for Sponsored Coastal Ocean Research ECOHAB program under award no. NA09NOS4780166 to the University of Texas Marine Science Institute (D.L.E) and the Woods Hole Center for Oceans and Human Health by National Science Foundation (NSF) award no. OCE-1314642 and National Institute of Environmental Health Sciences (NIEHS) award no. 1-P01-ES021923-014 to D.M.A. and M.L B

Rapid growth and concerted sexual transitions by a bloom of the harmful dinoflagellate Alexandrium fundyense (Dinophyceae)

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 60 (2015): 2059–2078, doi:10.1002/lno.10155.Transitions between life cycle stages by the harmful dinoflagellate Alexandrium fundyense are critical for the initiation and termination of its blooms. To quantify these transitions in a single population, an Imaging FlowCytobot (IFCB), was deployed in Salt Pond (Eastham, Massachusetts), a small, tidally flushed kettle pond that hosts near annual, localized A. fundyense blooms. Machine-based image classifiers differentiating A. fundyense life cycle stages were developed and results were compared to manually corrected IFCB samples, manual microscopy-based estimates of A. fundyense abundance, previously published data describing prevalence of the parasite Amoebophrya, and a continuous culture of A. fundyense infected with Amoebophrya. In Salt Pond, a development phase of sustained vegetative division lasted approximately 3 weeks and was followed by a rapid and near complete conversion to small, gamete cells. The gametic period (∼3 d) coincided with a spike in the frequency of fusing gametes (up to 5% of A. fundyense images) and was followed by a zygotic phase (∼4 d) during which cell sizes returned to their normal range but cell division and diel vertical migration ceased. Cell division during bloom development was strongly phased, enabling estimation of daily rates of division, which were more than twice those predicted from batch cultures grown at similar temperatures in replete medium. Data from the Salt Pond deployment provide the first continuous record of an A. fundyense population through its complete bloom cycle and demonstrate growth and sexual induction rates much higher than are typically observed in culture.National Science Foundation Grant Number: OCE-0430724, OCE-0911031, and OCE-1314642; National Institutes of Health Grant Number: NIEHS-1P50-ES021923-01; National Park Service (NPS) Cooperative Agreement Grant Number: H238015504; Gordon and Betty Moore Foundation Grant Number: #2649 to HMS; IOF Grant Number: MOHAB PIOF-GA-25226

LSU rDNA based RFLP assays for the routine identification of Gambierdiscus species

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Harmful Algae 66 (2017): 20-28, doi:10.1016/j.hal.2017.04.009.Gambierdiscus is a genus of benthic dinoflagellates commonly associated with ciguatera fish poisoning (CFP), which is generally found in tropical or sub-tropical regions around the world. Morphologically similar species within the genus can vary in toxicity; however, species identifications are difficult or sometimes impossible using light microscopy. DNA sequencing of ribosomal RNA genes (rDNA) is thus often used to identify and describe Gambierdiscus species and ribotypes, but the expense and time can be prohibitive for routine culture screening and/or large-scale monitoring programs. This study describes a restriction fragment length polymorphism (RFLP) typing method based on analysis of the large subunit ribosomal RNA gene (rDNA) that can successfully identify at least nine of the described Gambierdiscus species and two Fukuyoa species. The software programs DNAMAN 6.0 and Restriction Enzyme Picker were used to identify a set of restriction enzymes (SpeI, HpyCH4IV, and TaqαI) capable of distinguishing most of the known Gambierdiscus species for which DNA sequences were available. This assay was tested using in silico analysis and cultured isolates, and species identifications of isolates assigned by RFLP typing were confirmed by DNA sequencing. To verify the assay and assess intra-specific heterogeneity in RFLP patterns, identifications of 63 Gambierdiscus isolates comprising ten Gambierdiscus species, one ribotype, and two Fukuyoa species were confirmed using RFLP typing, and this method was subsequently employed in the routine identification of isolates collected from the Caribbean Sea. The RFLP assay presented here reduces the time and cost associated with morphological identification via scanning electron microscopy and/or DNA sequencing, and provides a phylogenetically sensitive method for routine Gambierdiscus species assignment.Funding for this study was provided by the U.S. National Oceanic and Atmospheric Administration ECOHAB program (CiguaHAB; Cooperative Agreement NA11NOS4780060, NA11NOS4780028), the China Scholarship Council and Natural Science Foundation of China (No. 41606137, 41606136), and the Guangxi Natural Science Foundation (2015GXNSFCA139003, 2016GXNSFBA380037)

Trojan horses in the marine realm: characterizing protistan parasite ecology in coastal waters

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.Research was supported by the WHOI Ocean Venture Fund, the National Science Foundation Biological Oceanography OCE-1851012, and the National Science Foundation Graduate Research Fellowship under Grant No. 1745302

Exploring the Diversity of Microeukaryotic Communities in New England Tide Pools

Though historically understudied, due in large part to most species being uncultivable, microbial eukaryotes (i.e. protists) are abundant and widespread across diverse habitats. Recent advances in molecular techniques, including metabarcoding, allow for the characterization of poorly known protist lineages. This study surveys the diversity of SAR (Stramenopila, Alveolata, and Rhizaria), a major eukaryotic clade that is estimated to represent about half of all eukaryotic diversity. SAR lineages use varied metabolic strategies like mixotrophy in dinoflagellates (Alveolata), parasitism in apicomplexans (Alveolata) and labyrinthulids (Stramenopila), and life cycle stages that include encystment and attachment (e.g. in ciliates, Alveolata) to survive in highly dynamic habitats. Using metabarcoding primers designed specifically to target a portion of the 18S small subunit ribosomal RNA (SSU-rRNA) gene of SAR lineages, we compare protist community composition from tide pools in Acadia National Park, Maine, USA. We characterize over 500 lineages, here operational taxonomic units (OTUs), many of which are found abundant in the tide pool environment. We also find that communities vary by month sampled and exhibit patterns by size (i.e. macro-, micro-, and nano-sized). Taken together, these data allow us to further catalog protist diversity in extreme environments (e.g. those subject to extreme fluctuations in temperature and salinity during tidal cycles). Such data are critical in the explorations of biodiversity patterns among microorganisms on our rapidly changing planet

Testate Amoebae (Arcellinida, Amoebozoa) Community Diversity in New England Bogs and Fens Assessed through Lineage-Specific Amplicon Sequencing

Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change

A randomised controlled trial to evaluate the impact of a human rights based approach to dementia care in inpatient ward and care home settings

BackgroundAlthough it is widely recognised that adopting a person-centred approach is beneficial in the care of people living with dementia, a gap remains between the rhetoric and the reality of quality care. Some widely adopted care practices can result in the personhood of this group being threatened and their human rights being undermined.ObjectivesTo evaluate the impact of applying a human rights based approach in dementia inpatient wards and care homes on the quality of care delivered and the well-being of the person living with dementia.DesignA cluster randomised design was employed to compare the impact of implementing a human rights based approach intervention (i.e. training, applying the ‘Getting It Right’ assessment tool and receiving booster sessions) at 10 intervention sites with 10 control sites.SettingEight NHS dementia inpatient wards and 12 care homes in the north-west of England.ParticipantsPeople living with dementia who were residing on dementia inpatient wards or in care homes, and staff working at these sites. The aim was to recruit 280 people living with dementia.InterventionsA sample of staff (an average of 8.9 per site) at each of the sites was trained in a human rights based approach to care, including the application of the ‘Getting It Right’ assessment tool. The tool was then introduced at the site and monthly booster sessions were delivered.Main outcome measuresThe primary outcome measure used in the research was the Quality of Life in Alzheimer’s Disease scale to assess the subjective well-being of the person with dementia. Secondary outcome measures included measures of the quality of care provided (dementia care mapping) and direct measures of the effectiveness of the training in increasing knowledge of and attitudes towards human rights. The study also included an economic evaluation utilising the EuroQol-5 Dimensions, three-level version, and the Adult Social Care Outcomes Toolkit measure.ResultsThe study recruited 439 people living with dementia: 213 to the intervention arm and 226 to the control arm. Primary outcome data were analysed using a linear mixed model. There were no significant differences found in the reported quality of life of residents between the control and intervention groups after the intervention [F(1,16.51) = 3.63;p = 0.074]. The mean difference between the groups was 1.48 (95% confidence interval –7.86 to 10.82).ConclusionsDespite the fact that the training increased staff knowledge of and positive attitudes towards human rights, and although there were some changes in staff decision-making strategies in clinical situations, there was no change in the quality of care provided or in the reported well-being of people living with dementia in these settings. This led to questions about the efficacy of training in bringing about cultural change and improving care practices.LimitationsThere was limited uptake of the training and booster sessions that were integral to the intervention.Future workFuture work could usefully focus on understanding the difficulty in translating change in attitude and knowledge into behaviour.Trial registrationCurrent Controlled Trials ISRCTN94553028.FundingThis project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full inHealth Services and Delivery Research; Vol. 6, No. 13. See the NIHR Journals Library website for further project information.</jats:sec

Trojan Horses in the Marine Realm: Characterizing Protistan Parasite Ecology in Coastal Waters

Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.Ph.D

Dufour_Arcellinida_LINSI_masked_95.tree

Tree used to assign taxonomy to Arcellinida OTUs</p

Trojan Horses in the Marine Realm: Characterizing Protistan Parasite Ecology in Coastal Waters

Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.Ph.D