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  • 1
    Electronic Resource
    Electronic Resource
    Saccamminid foraminifers from anoxic sediments: implications for Proterozoic ecosystem dynamics (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: Eukaryote origin and earliest diversification occurred in the Proterozoic when Earth's atmosphere was undoubtedly different from that of today. Atmospheric oxygen levels were increasing from the primordial anoxic atmosphere due, for example, to cyanobacterial oxygenic photosynthesis. Late Proterozoic (∼0.6–0.9 Gya) deep-ocean oxygen concentrations are less certain, but geochemical evidence suggests anoxia and hydrogen-sulfide enrichment. It can, therefore, be postulated that initial eukaryotic diversification occurred in oxygen-depleted, sulfide-enriched environments. Foraminifera are aerobes and, thus, not expected in anoxic settings. Recently, however, we found a saccamminid allogromian in a deep-water anoxic, sulfidic setting. Samples were collected from Santa Barbara Basin (California) when bottom-water oxygen was undetectable and sediments smelled strongly of hydrogen sulfide. Foraminiferal SSU rDNA sequences recovered from sediments included one from a previously uncharacterized saccamminid. Ultrastructural analysis indicated the presence of intact Golgi, mitochondria, and prokaryotic endobionts. Saccamminid occurrence in environmental conditions known to exist during the Proterozoic supports the possibility of their origin early in eukaryotic evolution. Extant saccamminids could have competed well in the prokaryote-dominated Proterozoic benthic ecosystem given their diet includes bacteria, bacterial biofilms and unicellular algae. Thus, Proterozoic foraminifers may have been top carnivores.Funded by NASA NRA-01-01-EXB-057, the Geological Society of America's W. Storrs Cole Memorial Research Award, and NSF OPP0003639.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_12.x
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  • 2
    Electronic Resource
    Electronic Resource
    The shell or the kernel: biodiversity estimates of benthic foraminifera (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: Estimates of protist biodiversity and distribution have until recently relied on the morphological identification of individual cells. The advent of environmental-DNA-based surveys of these protist communities has broadened our understanding of species richness and diversity. A “total-evidence biodiversity” approach gives two benefits. First, it allows “back-comparison” to previous studies of ecosystems, permitting estimates of the amount of cryptic diversity in different sampling regimes (and by extension, the fossil record). Second, it will provide the best possible estimate of the total species richness of current study sites. Here, we use a well-studied benthic protist community, the foraminiferal assemblage of McMurdo Sound, Antarctica, to determine the effective parameters of both detection methods. We find that molecular-based techniques detect well-characterized calcareous species at depths too great to allow calcification, suggesting that these forms may be able to survive without their distinctive tests. “Fragile” taxa also appear to be better represented in molecular surveys than in morphological ones. The strengths of a combined morphological–molecular approach are demonstrated by an assessment of the distribution of two species in the genus Notodendrodes; morphological detection excels in the identification of distinctive, patchily distributed adults, whereas molecular detection with taxon-specific probes enabled identification in less favorable sampling conditions. Such a “broad-plus-deep” approach appears to maximize detection efficiency in this Antarctic setting.Work supported by NSF OPP0003639.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_31.x
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  • 3
    Electronic Resource
    Electronic Resource
    Freshwater Foraminiferans Revealed by Analysis of Environmental DNA Samples (2003)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 50 (2003), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Sediment-dwelling protists are among the most abundant meiobenthic organisms, ubiquitous in all types of aquatic ecosystems. Yet, because their isolation and identification are difficult, their diversity remains largely unknown. In the present work, we applied molecular methods to examine the diversity of freshwater Foraminifera, a group of granuloreticulosan protists largely neglected until now. By using specific PCR primers, we detected the presence of Foraminifera in all sediment samples examined. Phylogenetic analysis of amplified SSU rDNA sequences revealed two distinct groups of freshwater foraminiferans. All obtained sequences branched within monothalamous (single-chambered), marine Foraminifera, suggesting a repeated colonization of freshwater environments. The results of our study challenge the traditional view of Foraminifera as essentially marine organisms, and provide a conceptual framework for charting the molecular diversity of freshwater granuloreticulosan protists.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2003.tb00248.x
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  • 4
    Electronic Resource
    Electronic Resource
    Divergent β-tubulins from foraminifera: Implications for microtubule assembly (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: Foraminifera utilize an unusual and very rapid microtubule assembly/disassembly system: a state transition between microtubules and helical filaments. The helical filament is an assembly polymorph that forms when the microtubule lattice uncoils into a ribbon of tubulin dimers connected only by lateral subunit/subunit bonds. An unusual β-tubulin sequence, which may be implicated in this process, has previously been reported from the foraminiferan Reticulomyxa filosa. In order to determine the taxonomic distribution and possible significance of this tubulin isoform, we sequenced and analyzed β-tubulin genes from a broad taxonomic range of foraminifera. These genes contain a large number of substitutions, conserved within the group, which may alter the biochemical properties of β-tubulin, especially in regions involved in subunit/subunit binding between α- and β-tubulin in the microtubule lattice. In particular, the M-loop, which is intimately involved in lateral subunit binding, shows only 30% homology to the consensus sequence for eukaryotic β-tubulins. Multiple regions identified to be involved in longitudinal contacts with α-tubulin are also highly substituted. In contrast, the foraminiferal α-tubulin is well conserved with its homologs in other organisms. We suggest that these alterations to the consensus eukaryotic β-tubulin sequence may help to explain the unusual assembly properties of foraminiferal microtubules.This work was supported by NSF OPP0003639.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_82.x
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  • 5
    Electronic Resource
    Electronic Resource
    Unexpected Foraminiferal Diversity Revealed by Small-subunit rDNA Analysis of Antarctic Sediment (2004)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 51 (2004), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Studies of benthic Foraminifera typically rely on the morphological identification of dried specimens. This approach can introduce sampling bias against small, delicate, or morphologically ambiguous forms. To overcome this limitation, we extracted total DNA from sediment followed by PCR using group- and species-specific primers. Phylogenetic analyses revealed that approximately ninety percent of the PCR products represented previously undescribed sequence types that group with undersampled members of the allogromiid Foraminifera. We also used a modification of this technique to track individual species in sediment fractions too fine for normal morphological identification, and to confirm species placement of morphologically ambiguous foraminiferans. We were able to identify the DNA of several large foraminiferal species in fine fractions in a seasonally-dependent manner, indicating that in some seasons the majority of the standing stock of these species exists as gametes/juveniles. The approach outlined here represents a powerful strategy for exploring the total diversity of benthic foraminiferal communities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2004.tb00542.x
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  • 6
    Electronic Resource
    Electronic Resource
    Foraminiferal evolution as revealed by β-tubulin data (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: Foraminiferal taxonomy is traditionally based on morphological characteristics, particularly the structure and composition of the test (shell). Recently, a comprehensive SSU-based molecular phylogeny confirmed some multi-chambered foraminiferal groups while enhancing our understanding of the single-chambered, or the so-called “allogromiid”, taxa. However, some relationships, such as the origin of the foraminiferal order Miliolida, remain unresolved, suggesting an approach involving multiple data sources may improve understanding. Here, we discuss the evolutionary implications of β-tubulin genes from several species of foraminifera. Foraminiferal β-tubulin is highly divergent, possibly indicating a period of accelerated evolution of this gene at the base of the foraminiferal lineage, but it is well-conserved within the group. We show its utility in helping to resolve the phylogenetic position of Miliammina fusca, a foraminiferan whose proper classification has been debated for 70 years. M. fusca is a morphological “chimera”, and we show that its placement in SSU trees is not particularly robust. However, β-tubulin data assigns Miliammina to the Miliolida, some of whose members show a similar chamber coiling pattern. This placement agrees with an earlier observation that M. fusca's actin isoforms more closely resemble those of traditional milolids. This finding implies that test formation can revert from calcareous to agglutinated, suggesting a reexamination of some relationships inferred from the fossil record.Supported by NSF OPP0003639.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_32.x
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  • 7
    Electronic Resource
    Electronic Resource
    Predicted Secondary Structure of the Foraminiferal SSU 3′ Major Domain Reveals a Molecular Synapomorphy for Granuloreticulosean Protists (2004)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 51 (2004), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The small subunit ribosomal RNA genes of foraminiferal protists are the largest and most divergent of any eukaryote. We demonstrate that this foraminiferal sequence alteration represents a substantial modification to the small subunit ribosomal RNA structure, including a large (up to 350 nt) novel helix in a very well-conserved portion of the head domain. This modification dates from the beginning of the foraminiferal radiation and, within modern orders, is partially conserved at the sequence level, suggesting that it is a functional part of the ribosome. The pattern of conservation makes it particularly useful for determining lower-taxon relationships in morphologically ambiguous allogromiid foraminifera.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2004.tb00397.x
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  • 8
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    An endobiont-bearing allogromiid from the Santa Barbara Basin : implications for the early diversification of foraminifera (2006)
    American Geophysical Union
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): G03002, doi:10.1029/2005JG000158.
    Description: Our current understanding of paleoecology and paleoceanography is largely based on the superb Phanerozoic fossil record of foraminiferan protists. The early history of the group is unresolved, however, because basal foraminiferans (allogromiids) are unmineralized and thus fossilize poorly. Molecular-clock studies date foraminiferal origins to the Neoproterozoic, but the deep sea – one of Earth’s most extensive habitats and presently a significant fraction of basal foraminiferal diversity— was probably anoxic at that time and, until now, anaerobic allogromiids were unknown. Molecular, cell and ecological analyses reveal the presence of a previously unknown allogromiid inhabiting anoxic, sulfidic deep-sea sediments (Santa Barbara Basin, California, USA). The fact that the new foraminifer harbors prokaryotic endobionts implicates symbiogenesis as a driving force in early foraminiferal diversification.
    Description: The Wadsworth Center’s Electron Microscopy, Biochemistry, and Molecular Genetics Core facilities, as well as its National Biotechnology Resource for the Visualization of Biological Complexity (supported by a NIH BRTP/NCRR grant) are gratefully acknowledged. Funded by NASA Exobiology NRA-01-01-EXB-057 (to J.M.B.); W. Storrs Cole Memorial Research Award (Geological Society of America, to J.M.B.); NSF DEB0445181 (to S.S.B.).
    Keywords: Foraminifera ; Santa Barbara Basin ; Symbiosis
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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