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  • 1
    Online Resource
    Online Resource
    Emerging harmful algal blooms caused by distinct seasonal assemblages of a toxic diatom
    Wiley ; 2022
    In:  Limnology and Oceanography Vol. 67, No. 11 ( 2022-11), p. 2341-2359
    Details
    In: Limnology and Oceanography, Wiley, Vol. 67, No. 11 ( 2022-11), p. 2341-2359
    Abstract: Diatoms in the Pseudo‐nitzschia genus produce the neurotoxin domoic acid. Domoic acid bioaccumulates in shellfish, causing illness in humans and marine animals upon ingestion. In 2017, high domoic acid levels in shellfish meat closed shellfish harvest in Narragansett Bay, Rhode Island for the first and only time in history, although abundant Pseudo‐nitzschia have been observed for over 60 years . To investigate whether an environmental factor altered endemic Pseudo‐nitzschia physiology or new domoic acid‐producing strain(s) were introduced to Narragansett Bay, we conducted weekly sampling from 2017 to 2019 and compared closure samples. Plankton‐associated domoic acid was quantified by LC‐MS/MS and Pseudo‐nitzschia spp. were identified using a taxonomically improved high‐throughput rDNA sequencing approach. Comparison with environmental data revealed a detailed understanding of domoic acid dynamics and seasonal multi‐species assemblages. Plankton‐associated domoic acid was low throughout 2017–2019, but recurred in fall and early summer maxima. Fall domoic acid maxima contained known toxic species as well as a novel Pseudo‐nitzschia genotype. Summer domoic acid maxima included fewer species but also known toxin producers . Most 2017 closure samples contained the particularly concerning toxic species, P. australis , which also appeared infrequently during 2017–2019. Recurring Pseudo‐nitzschia assemblages were driven by seasonal temperature changes, and plankton‐associated domoic acid correlated with low dissolved inorganic nitrogen. Thus, the Narragansett Bay closures were likely caused by both resident assemblages that become toxic depending on nutrient status as well as the episodic introductions of toxic species from oceanographic and climatic shifts.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v67.11
    DOI: 10.1002/lno.12189
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2033191-5
    detail.hit.zdb_id: 412737-7
    SSG: 12
    SSG: 14
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  • 2
    Online Resource
    Online Resource
    Novel glucocorticoid receptor coactivator effector mechanisms
    Elsevier BV ; 2001
    In:  Trends in Endocrinology & Metabolism Vol. 12, No. 3 ( 2001-4), p. 122-126
    Details
    In: Trends in Endocrinology & Metabolism, Elsevier BV, Vol. 12, No. 3 ( 2001-4), p. 122-126
    Type of Medium: Online Resource
    ISSN: 1043-2760
    URL: Article
    DOI: 10.1016/S1043-2760(00)00357-X
    RVK:
    XA 10000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2001
    detail.hit.zdb_id: 1499104-4
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  • 3
    Online Resource
    Online Resource
    The Genome of the Diatom Thalassiosira Pseudonana : Ecology, Evolution, and Metabolism
    American Association for the Advancement of Science (AAAS) ; 2004
    In:  Science Vol. 306, No. 5693 ( 2004-10), p. 79-86
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 306, No. 5693 ( 2004-10), p. 79-86
    Abstract: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ∼20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1101156
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2004
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 4
    Online Resource
    Online Resource
    Development and Testing of a DNA Macroarray To Assess Nitrogenase ( nifH ) Gene Diversity
    American Society for Microbiology ; 2004
    In:  Applied and Environmental Microbiology Vol. 70, No. 3 ( 2004-03), p. 1455-1465
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 70, No. 3 ( 2004-03), p. 1455-1465
    Abstract: A DNA macroarray was developed and evaluated for its potential to distinguish variants of the dinitrogenase reductase ( nifH ) gene. Diverse nifH gene fragments amplified from a clone library were spotted onto nylon membranes. Amplified, biotinylated nifH fragments from individual clones or a natural picoplankton community were hybridized to the array and detected by chemiluminescence. A hybridization test with six individual targets mixed in equal proportions resulted in comparable relative signal intensities for the corresponding probes (standard deviation, 14%). When the targets were mixed in unequal concentrations, there was a predictable, but nonlinear, relationship between target concentration and relative signal intensity. Results implied a detection limit of roughly 13 pg of target ml −1 , a half-saturation of signal at 0.26 ng ml −1 , and a dynamic range of about 2 orders of magnitude. The threshold for cross-hybridization varied between 78 and 88% sequence identity. Hybridization patterns were reproducible with significant correlations between signal intensities of duplicate probes ( r = 0.98, P 〈 0.0001, n = 88). A mixed nifH target amplified from a natural Chesapeake Bay water sample hybridized strongly to 6 of 88 total probes and weakly to 17 additional probes. The natural community results were well simulated ( r = 0.941, P 〈 0.0001, n = 88) by hybridizing a defined mixture of six individual targets corresponding to the strongly hybridizing probes. Our results indicate that macroarray hybridization can be a highly reproducible, semiquantitative method for assessing the diversity of functional genes represented in mixed pools of PCR products amplified from the environment.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.70.3.1455-1465.2004
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Fingerprinting Diazotroph Communities in the Chesapeake Bay by Using a DNA Macroarray
    American Society for Microbiology ; 2004
    In:  Applied and Environmental Microbiology Vol. 70, No. 3 ( 2004-03), p. 1767-1776
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 70, No. 3 ( 2004-03), p. 1767-1776
    Abstract: Investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on PCR amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifH . Recent work has suggested that DNA macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifH amplicons (G. F. Steward, B. D. Jenkins, B. B. Ward, and J. P. Zehr, Appl. Environ. Microbiol. 70:1455-1465, 2004). Here we report the application of macroarrays for a study in the Chesapeake Bay. Samples from different locations in the bay yielded distinct fingerprints. Analysis of replicates and samples from different locations by cluster analysis showed that replicates clustered together, whereas different samples formed distinct clusters. There was a correspondence between the hybridization pattern observed and that predicted from the distribution of sequence types in a corresponding clone library. Some discrepancies between the methods were observed which are likely a result of the high nifH sequence diversity in the Chesapeake Bay and the limited number of sequences represented on this version of the array. Analyses of sequences in the clone library indicate that the Chesapeake Bay harbors unique, phylogenetically diverse diazotrophs. The macroarray hybridization patterns suggest that there are spatially variable communities of diazotrophs, which have been confirmed by quantitative PCR methods (S. M. Short, B. D. Jenkins, and J. P. Zehr, Appl. Environ. Microbiol., in press). The results show that DNA macroarrays have great potential for mapping the spatial and temporal variability of functional gene diversity in the environment.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.70.3.1767-1776.2004
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Spatial and Temporal Distribution of Two Diazotrophic Bacteria in the Chesapeake Bay
    American Society for Microbiology ; 2004
    In:  Applied and Environmental Microbiology Vol. 70, No. 4 ( 2004-04), p. 2186-2192
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 70, No. 4 ( 2004-04), p. 2186-2192
    Abstract: The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10 7 gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml −1 and the maximum number of 912h4 gene copies detected was approximately 340 ml −1 . Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.70.4.2186-2192.2004
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Genetic indicators of iron limitation in wild populations of Thalassiosira oceanica from the northeast Pacific Ocean
    Springer Science and Business Media LLC ; 2015
    In:  The ISME Journal Vol. 9, No. 3 ( 2015-3), p. 592-602
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 9, No. 3 ( 2015-3), p. 592-602
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/ismej.2014.171
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2299378-2
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  • 8
    Online Resource
    Online Resource
    DataSheet_1.docx
    Frontiers Media SA ; 2023
    In:  Frontiers in Marine Science Vol. 9 ( 2023-3-2)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 9 ( 2023-3-2)
    Abstract: The growth of diatoms in the Southern Ocean, especially the region surrounding the West Antarctic Peninsula, is frequently constrained by low dissolved iron and other trace metal concentrations. This challenge may be overcome by mutualisms between diatoms and co-occurring associated bacteria, in which diatoms produce organic carbon as a substrate for bacterial growth, and bacteria produce siderophores, metal-binding ligands that can supply diatoms with metals upon uptake as well as other useful secondary compounds for diatom growth like vitamins. To examine the relationships between diatoms and bacteria in the plankton (diatom) size class ( & gt; 3 µm), we sampled both bacterial and diatom community composition with accompanying environmental metadata across a naturally occurring concentration gradient of macronutrients, trace metals and siderophores at 21 stations near the West Antarctic Peninsula (WAP). Offshore Drake Passage stations had low dissolved iron (0.33 ± 0.15 nM), while the stations closer to the continental margin had higher dissolved iron (5.05 ± 1.83 nM). A similar geographic pattern was observed for macronutrients and most other trace metals measured, but there was not a clear inshore-offshore gradient in siderophore concentrations. The diatom and bacteria assemblages, determined using 18S and 16S rDNA sequencing respectively, were similar by location sampled, and variance in both assemblages was driven in part by concentrations of soluble reactive phosphorous, dissolved manganese, and dissolved copper, which were all higher near the continent. Some of the most common diatom sequence types observed were Thalassiosira and Fragilariopsis , and bacteria in the plankton size fraction were most commonly Bacteroidetes and Gammaproteobacteria. Network analysis showed positive associations between diatoms and bacteria, indicating possible in situ mutualisms through strategies such as siderophore and vitamin biosynthesis and exchange. This work furthers the understanding of how naturally occurring gradients of metals and nutrients influence diatom-bacteria interactions. Our data suggest that distinct groups of diatoms and associated bacteria are interacting under different trace metal regimes in the WAP, and that diatoms with different bacterial partners may have different modes of biologically supplied trace metals.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    URL: Article
    DOI: 10.3389/fmars.2022.876830
    DOI: 10.3389/fmars.2022.876830.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2757748-X
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  • 9
    Online Resource
    Online Resource
    Application of a nifH oligonucleotide microarray for profiling diversity of N 2 ‐fixing microorganisms in marine microbial mats
    Wiley ; 2006
    In:  Environmental Microbiology Vol. 8, No. 10 ( 2006-10), p. 1721-1735
    Details
    In: Environmental Microbiology, Wiley, Vol. 8, No. 10 ( 2006-10), p. 1721-1735
    Abstract: Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety‐six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7‐month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2006.8.issue-10
    DOI: 10.1111/j.1462-2920.2006.01108.x
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Nitrogenase gene diversity and microbial community structure: a cross‐system comparison
    Wiley ; 2003
    In:  Environmental Microbiology Vol. 5, No. 7 ( 2003-07), p. 539-554
    Details
    In: Environmental Microbiology, Wiley, Vol. 5, No. 7 ( 2003-07), p. 539-554
    Abstract: Biological nitrogen fixation is an important source of fixed nitrogen for the biosphere. Microorganisms catalyse biological nitrogen fixation with the enzyme nitrogenase, which has been highly conserved through evolution. Cloning and sequencing of one of the nitrogenase structural genes, nifH , has provided a large, rapidly expanding database of sequences from diverse terrestrial and aquatic environments. Comparison of nifH phylogenies to ribosomal RNA phylogenies from cultivated microorganisms shows little conclusive evidence of lateral gene transfer. Sequence diversity far outstrips representation by cultivated representatives. The phylogeny of nitrogenase includes branches that represent phylotypic groupings based on ribosomal RNA phylogeny, but also includes paralogous clades including the alternative, non‐molybdenum, non‐vanadium containing nitrogenases. Only a few alternative or archaeal nitrogenase sequences have as yet been obtained from the environment. Extensive analysis of the distribution of nifH phylotypes among habitats indicates that there are characteristic patterns of nitrogen fixing microorganisms in termite guts, sediment and soil environments, estuaries and salt marshes, and oligotrophic oceans. The distribution of nitrogen‐fixing microorganisms, although not entirely dictated by the nitrogen availability in the environment, is non‐random and can be predicted on the basis of habitat characteristics. The ability to assay for gene expression and investigate genome arrangements provides the promise of new tools for interrogating natural populations of diazotrophs. The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Article
    DOI: 10.1046/j.1462-2920.2003.00451.x
    Language: English
    Publisher: Wiley
    Publication Date: 2003
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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