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  • 1
    Electronic Resource
    Electronic Resource
    Subgenus Systematics of Acanthamoeba: Four Nuclear 18S rDNA Sequence Types (1996)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 43 (1996), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Classification of Acanthamoeba at the subgenus level has been problematic, but increasing reports of Acanthamoeba as an opportunistic human pathogen have generated an interest in finding a more consistent basis for classification. Thus, we are developing a classification scheme based on RNA gene sequences. This first report is based on analysis of complete sequences of nuclear small ribosomal subunit RNA genes (Rns) from 18 strains. Sequence variation was localized in 12 highly variable regions. Four distinct sequence types were identified based on parsimony and distance analyses. Three were obtained from single strains: Type T1 from Acanthamoeba castellanii V006, T2 from Acanthamoeba palestinensis Reich, and T3 from Acanthamoeba griffini S-7. T4, the fourth sequence type, included 15 isolates classified as A. castellanii, Acanthamoeba polyphaga, Acanthamoeba rhysodes, or Acanthamoeba sp., and included all 10 Acanthamoeba keratitis isolates. Interstrain sequence differences within T4 were 0%–4.3%, whereas differences among sequence types were 6%–12%. Branching orders obtained by parsimony and distance analyses were inconsistent with the current classification of T4 strains and provided further evidence of a need to reevaluate criteria for classification in this genus. Based on this report and others in preparation, we propose that Rns sequence types provide the consistent quantititive basis for classification that is needed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1996.tb04510.x
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  • 2
    Electronic Resource
    Electronic Resource
    Antarctic amoebae adventures (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Ice, slush, sediment and water samples were collected from the Ross Sea, Antarctica and enriched with a variety of inorganic and organic nutrients. All cultures were maintained at an ambient temperature of 1°C, and amoebae were observed to occur in the slush, sediment and water enrichments. Amoebae were isolated into clonal or monocultures, and their characterization was accomplished using a combination of molecular and morphological methods. Full-length 18S ribosomal DNA sequence data indicated that seven of the isolates represented four different amoebae of the Vexilliferidae and Vannellidae families. Acquisition of 18S ribosomal sequences from the parasomes of two amoebae further confirmed their identification as Neoparamoeba species. Light microscopy, fluorescence microscopy and TEM observations were accomplished and further support the molecular data. To determine whether these amoebae represented psychrophilic strains, their temperature tolerances were tested. Cultures were inoculated at 1°C and the temperature was raised 1°C/day (to a total of 5°), and then held at that temperature for 6 days. This pattern was repeated in 5°-increments, up to 20°C. The cultures were observed frequently for death and possible cyst formation. Three (2 types of Vannellids) out of seven amoeba cultures survived up to 20°C. Whereas, the two different Vexilliferids died at a range of temperatures between 10°C and 20°C. These data indicate that amoebae found in the Antarctic are varied in their physiological adaptation for growth at cold temperatures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_62.x
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  • 3
    Electronic Resource
    Electronic Resource
    The Evolutionary History of the Genus Acanthamoeba and the Identification of Eight New 18S rRNA Gene Sequence Types (1998)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 45 (1998), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The 18S rRNA gene (Rns) phylogeny of Acanthamoeba is being investigated as a basis for improvements in the nomenclature and taxonomy of the genus. We previously analyzed Rns sequences from 18 isolates from morphological groups 2 and 3 and found that they fell into four distinct evolutionary lineages we called sequence types T1-T4. Here, we analyzed sequences from 53 isolates representing 16 species and including 35 new strains. Eight additional lineages (sequence types T5-T12) were identified. Four of the 12 sequence types included strains from more than one nominal species. Thus, sequence types could be equated with species in some cases or with complexes of closely related species in others. The largest complex, sequence type T4, which contained six closely related nominal species, included 24 of 25 keratitis isolates. Rns sequence variation was insufficient for full phylogenetic resolution of branching orders within this complex, but the mixing of species observed at terminal nodes confirmed that traditional classification of isolates has been inconsistent. One solution to this problem would be to equate sequence types and single species. Alternatively, additional molecular information will be required to reliably differentiate species within the complexes. Three sequence types of morphological group 1 species represented the earliest divergence in the history of the genus and, based on their genetic distinctiveness, are candidates for reclassification as one or more novel genera.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1998.tb05068.x
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  • 4
    Electronic Resource
    Electronic Resource
    Protistan diversity in the Ross Sea, Antarctica: linking genotype, morphology and physiology (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Traditional microscope-based studies of protistan assemblages in the Ross Sea, Antarctica have contributed significantly to our understanding of the microbial biogeography and food web structure in this extreme cold-water environment. However, these investigations have neither been able to characterize the genetic diversity of the communities, nor have they necessarily determined the abundances or trophic contribution of the dominant organisms. Resolution of the latter issue is hindered by the fact that physiological studies are often conducted on opportunistic species that respond to enrichment culture rather than species truly representative of intact communities. Therefore, we sought to determine the genetic diversity of microbial eukaryotes in ice, water and slush samples from the Ross Sea, and establish both morphologic and physiologic links between enrichment cultures and the genetic data. Denaturing gradient gel electrophoresis and ribosomal clone library analyses indicate that the protistan communities are very diverse, but those present in similar habitats are more alike than those in different habitats at the same site. We have been able to identify several protists from our enrichment cultures as being genetically represented in the original samples. General studies of their physiology have been initiated and methods for determining their abundances are being developed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_28.x
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  • 5
    Electronic Resource
    Electronic Resource
    Protistan Diversity Estimates Based on 18S rDNA from Seawater Incubations in the Western North Atlantic (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract. Cloning/sequencing and fragment analysis of ribosomal RNA genes (rDNA) are becoming increasingly common methods for the identification of microbial taxa. Sequences of these genes provide many additional taxonomic characters for species that otherwise have few distinctive morphological features, or that require involved microscopy or laboratory culture and testing. These same approaches are now being applied with great success in ecological studies of natural communities of microorganisms. Extensive information on the composition of natural microbial assemblages is being amassed at a rapid pace through genetic analyses of environmental samples and comparison of the resulting genetic information with well-established (and rapidly growing) public databases. We examined microbial eukaryote diversity in a natural seawater sample from the coastal western North Atlantic Ocean using two molecular biological approaches: the cloning and sequencing of rRNA genes and by fragment analysis of these genes using the terminal restriction fragment length polymorphism (T-RFLP) method. A simple experiment was carried out to examine changes in the overall eukaryote (largely protistan) diversity and species composition (phylotype diversity) of a natural microbial assemblage when a seawater sample is placed in a container and incubated at ambient light and temperature for 72 h. Containment of the natural seawater sample resulted in relatively minor changes in the overall eukaryote diversity (species richness) obtained by either molecular method at three time points (time-zero, time-24 h, time-72 h). However, substantial changes in the dominance of particular eukaryote phylotypes took place between the three sampling times. Only 18% of the total number of phylotypes observed in the study were observed at all three time points, while 65% (108 of 165) phylotypes were observed only at a single time point (54 unique phylotypes initially, 37 more unique phylotypes at 24 h, and 17 more at 72 h). The results of this study indicate that a high diversity of protistan taxa existed in the original seawater sample at very low abundance, and thus were not observed in the initial characterization of community structure. Containment resulted in significant shifts in the dominance of these taxa, enabling the presence of previously unobserved phylotypes to be documented after 24 or 72 h of incubation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202006.x
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  • 6
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    A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis (2019)
    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 116 (36). pp. 17934-17942.
    Details
    Publication Date: 2022-01-31
    Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1073/pnas.1910121116
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 7
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    The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs (2021)
    In:  jill.stewart@unc.edu | http://aquaticcommons.org/id/eprint/14915 | 403 | 2014-03-10 19:59:25 | 14915 | United States National Ocean Service
    Details
    Publication Date: 2021-06-28
    Description: Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.
    Description: Article includes 14 pages.
    Keywords: Environment ; Health ; Management
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: S3
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  • 8
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    Defining DNA-based operational taxonomic units for microbial-eukaryote ecology (2010)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 75 (2009): 5797-5808, doi:10.1128/AEM.00298-09.
    Description: DNA sequence information has been increasingly used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, the autecology of ecologically relevant species, and the identification and enumeration of species of interest to human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is partly a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes, and partly the problematic nature and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximate species-level distinctions. The approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small subunit ribosomal RNA (18S) gene sequences and partial gene sequences obtained from GenBank for morphologically described protistan species. The program was tested using environmental 18S data sets from two oceanic ecosystems. A total of 388 operational taxonomic units were observed among 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific.
    Description: Support for this manuscript was provided by National Science Foundation grants MCB-0732066, MCB-0703159 and OCE-0550829 and a grant from the Gordon and Betty Moore Foundation.
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 9
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    Marine vertebrate zoonoses : an overview of the DAO Special Issue (2011)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Diseases of Aquatic Organisms 81 (2008): 1-3, doi:10.3354/dao01940.
    Description: The role of marine birds, mammals, turtles and fish as vectors of infectious agents of potential risk to humans can be examined from a variety of perspectives. The studies in this DAO Special include a broad survey of multiple agents and species, a sequencing study of Giardia intestinalis haplotypes known to be pathogenic to humans, an assessment of risks to humans working with marine mammals, a source tracking study using E. coli ribotypes, studies of regional Salmonella and Brucella epizootiology, a serology survey and a case report of a herpes simplex infection in a dolphin. Additionally, a recently published study (Venn-Watson et al. 2008; Dis Aquat Org 79:87–93) classifying pure cultures of bacteria from a captive dolphin colony also pertains to this theme. These studies raise the following questions: whether the presence of zoonotic agents in marine vertebrates represents a risk to other marine vertebrates, humans, or both; what are the routes by which these marine vertebrate zoonotic infections are acquired and circulated in the marine ecosystem; to what degree are such agents subclinical versus causes of overt disease in marine vertebrates; what are the subsets of the human population most likely to be affected by such infections; and which human health preventive measures would seem reasonable?
    Keywords: Zoonosis ; Marine ; Vertebrate
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 10
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    Environmental distribution and persistence of Quahog Parasite Unknown (QPX) (2013)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Diseases of Aquatic Organisms 81 (2008): 219-229, doi:10.3354/dao01948.
    Description: Quahog Parasite Unknown (QPX) is the cause of mass mortality events of hard clams Mercenaria mercenaria from Virginia, USA, to New Brunswick, Canada. Aquaculture areas in Massachusetts, USA, have been particularly hard hit. The parasite has been shown to be a directly infective organism, but it is unclear whether it could exist or persist outside of its clam host. We used molecular methods to examine water, sediment, seaweeds, seagrass and various invertebrates for the presence of QPX. Sites in Virginia and Massachusetts were selected based upon the incidence of QPX-induced clam die-offs, and they were monitored seasonally. QPX was detectable in almost all of our different sample types from Massachusetts, indicating that the parasite was widely distributed in the environment. Significantly more samples from Massachusetts were positive than from Virginia, and there was a seasonal pattern to the types of samples positive from Massachusetts. The data suggest that, although it may be difficult to completely eradicate QPX from the environment, it may be possible to keep the incidence of disease under control through good plot husbandry and the removal of infected and dying clams.
    Description: This work is the result of research sponsored by NOAA National Sea Grant College Program Office, Department of Commerce, under Grant No. NA16RG2273, Woods Hole Oceanographic Institution Sea Grant Project No. R/B-168.
    Keywords: Quahog Parasite Unknown ; QPX ; Environmental detection ; Remediation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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