GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    Diversity of the Microeukaryotic Community in Sulfide-Rich Zodletone Spring (Oklahoma)
    American Society for Microbiology ; 2005
    In:  Applied and Environmental Microbiology Vol. 71, No. 10 ( 2005-10), p. 6175-6184
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 71, No. 10 ( 2005-10), p. 6175-6184
    Abstract: The microeukaryotic community in Zodletone Spring, a predominantly anaerobic sulfide and sulfur-rich spring, was examined using an 18S rRNA gene cloning and sequencing approach. The majority of the 288 clones sequenced from three different locations at Zodletone Spring belonged to the Stramenopiles , Alveolata , and Fungi , with members of the phylum Cercozoa , order Diplomonadida , and family Jakobidae representing a minor fraction of the clone library. No sequences suggesting the presence of novel kingdom level diversity were detected in any of the three libraries. A large fraction of stramenopile clones encountered were monophyletic with either members of the genus Cafeteria (order Bicosoecida ) or members of the order Labyrinthulida (slime nets), both of which have so far been encountered mainly in marine habitats. The majority of the observed fungal clone sequences belonged to the ascomycetous yeasts (order Saccharomycetales ), were closely related to yeast genera within the Hymenobasidiomycetes (phylum Basidiomycetes ), or formed a novel fungal lineage with several previously published or database-deposited clones. To determine whether the unexpected abundance of fungal sequences in Zodletone Spring clone libraries represents a general pattern in anaerobic habitats, we generated three clone libraries from three different anaerobic settings (anaerobic sewage digester, pond sediment, and hydrocarbon-exposed aquifer sediments) and partially sequenced 210 of these clones. Phylogenetic analysis indicated that clone sequences belonging to the kingdom Fungi represent a significant fraction of all three clone libraries, an observation confirmed by phospholipid fatty acid and ergosterol analysis. Overall, this work reveals an unexpected abundance of Fungi in anaerobic habitats, describes a novel, yet-uncultured group of Fungi that appears to be widespread in anaerobic habitats, and indicates that several of the previously considered marine protists could also occur in nonmarine habitats.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.71.10.6175-6184.2005
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer
    American Society for Microbiology ; 2007
    In:  Applied and Environmental Microbiology Vol. 73, No. 15 ( 2007-08), p. 4892-4904
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 73, No. 15 ( 2007-08), p. 4892-4904
    Abstract: Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate ( 〉 130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria . Clone libraries derived from dissimilatory nitrite reductase genes ( nirK and nirS ) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00331-07
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2007
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere
    American Society for Microbiology ; 2008
    In:  Applied and Environmental Microbiology Vol. 74, No. 17 ( 2008-09), p. 5422-5428
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 74, No. 17 ( 2008-09), p. 5422-5428
    Abstract: Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00410-08
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2008
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    Desulfoferrobacter suflitae gen. nov., sp. nov., a novel sulphate-reducing bacterium in the Deltaproteobacteria capable of autotrophic growth with hydrogen or elemental iron
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 8 ( 2022-08-12)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 8 ( 2022-08-12)
    Abstract: A mesophilic sulphate-reducing micro-organism, able to grow chemolithoautotrophically with H 2 /CO 2 (20 : 80) and with elemental iron as a sole electron donor, was isolated from a consortium capable of degrading long-chain paraffins and designated strain DRH4 T . Cells were oval shaped often with bright refractile cores and occurred singly or in pairs. The cells formed pili. Strain DRH4 T could grow chemolithoautotrophically with H 2 /CO 2 or elemental iron and chemoorganotrophically utilizing a number of organic substrates, such as fatty acids from formate to octanoate (C 1 –C 8 ). Sulphate and thiosulphate served as terminal electron acceptors, but sulphite and nitrate did not. Optimal growth was observed from 37 to 40 °C and pH from 6.5 to 7.2. Strain DRH4 T did not require NaCl for growth and could proliferate under a broad range of salinities from freshwater (1 g l −1 NaCl) to seawater (27 g l −1 NaCl) conditions. The genomic DNA G+C content was 54.46 mol %. Based on 16S rRNA gene sequence analysis. strain DRH4 T was distinct from previously described Deltaproteobacteria species exhibiting the closest affiliation to Desulforhabdus amnigena ASRB1 T , Syntrophobacterium sulfatireducens TB8106 T and Desulfovirga adipica 12016 T with 93.35, 93.42 and 92.85 % similarity, respectively. Strain DRH4 T showed significant physiological differences with the aforementioned organisms. Based on physiological differences and phylogenetic comparisons, we propose to classify DRH4 T as the type strain (=DSM 113 455 T =JCM 39 248 T ) of a novel species of a new genus with the name Desulfoferrobacter suflitae gen. nov., sp. nov.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005483
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 5
    Online Resource
    Online Resource
    Supplemental Information 2: Fasta Files
    PeerJ ; 2017
    In:  PeerJ Vol. 5 ( 2017-04-04), p. e3161-
    Details
    In: PeerJ, PeerJ, Vol. 5 ( 2017-04-04), p. e3161-
    Abstract: The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.7717/peerj.3161
    DOI: 10.7717/peerj.3161/fig-1
    DOI: 10.7717/peerj.3161/fig-2
    DOI: 10.7717/peerj.3161/fig-3
    DOI: 10.7717/peerj.3161/fig-4
    DOI: 10.7717/peerj.3161/fig-5
    DOI: 10.7717/peerj.3161/fig-6
    DOI: 10.7717/peerj.3161/supp-1
    DOI: 10.7717/peerj.3161/supp-2
    Language: English
    Publisher: PeerJ
    Publication Date: 2017
    detail.hit.zdb_id: 2703241-3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 6
    Online Resource
    Online Resource
    A novel conjugative plasmid from Enterococcus faecalis E99 enhances resistance to ultraviolet radiation
    Elsevier BV ; 2010
    In:  Plasmid Vol. 64, No. 1 ( 2010-7), p. 18-25
    Details
    In: Plasmid, Elsevier BV, Vol. 64, No. 1 ( 2010-7), p. 18-25
    Type of Medium: Online Resource
    ISSN: 0147-619X
    URL: Article
    DOI: 10.1016/j.plasmid.2010.03.001
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2010
    detail.hit.zdb_id: 1471554-5
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 7
    Online Resource
    Online Resource
    Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole
    Elsevier BV ; 2016
    In:  Nitric Oxide Vol. 60 ( 2016-11), p. 32-39
    Details
    In: Nitric Oxide, Elsevier BV, Vol. 60 ( 2016-11), p. 32-39
    Type of Medium: Online Resource
    ISSN: 1089-8603
    URL: Article
    DOI: 10.1016/j.niox.2016.09.003
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 1471433-4
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 8
    Online Resource
    Online Resource
    Complete genome sequence of an M1 strain of Streptococcus pyogenes
    Proceedings of the National Academy of Sciences ; 2001
    In:  Proceedings of the National Academy of Sciences Vol. 98, No. 8 ( 2001-04-10), p. 4658-4663
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 98, No. 8 ( 2001-04-10), p. 4658-4663
    Abstract: The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes , a Gram-positive pathogen, has been determined and contains 1,752 predicted protein-encoding genes. Approximately one-third of these genes have no identifiable function, with the remainder falling into previously characterized categories of known microbial function. Consistent with the observation that S. pyogenes is responsible for a wider variety of human disease than any other bacterial species, more than 40 putative virulence-associated genes have been identified. Additional genes have been identified that encode proteins likely associated with microbial “molecular mimicry” of host characteristics and involved in rheumatic fever or acute glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes is also present, with each containing genes for one or more previously undiscovered superantigen-like proteins. These prophage-associated genes encode at least six potential virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer and a possible mechanism for generating new strains with increased pathogenic potential.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.071559398
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2001
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 9
    Online Resource
    Online Resource
    Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress
    Springer Science and Business Media LLC ; 2014
    In:  BMC Genomics Vol. 15, No. 1 ( 2014), p. 591-
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 2014), p. 591-
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/1471-2164-15-591
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 2041499-7
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 10
    Online Resource
    Online Resource
    Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies
    American Society for Microbiology ; 2021
    In:  mSystems Vol. 6, No. 5 ( 2021-10-26)
    Details
    In: mSystems, American Society for Microbiology, Vol. 6, No. 5 ( 2021-10-26)
    Abstract: The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria , different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature’s metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery. IMPORTANCE Natural product drug discovery efforts rely on libraries of organisms to provide access to diverse pools of compounds. Actionable strategies to rationally maximize chemical diversity, rather than relying on serendipity, can add value to such efforts. Readily implementable biological (i.e., ITS sequence analysis) and chemical (i.e., mass spectrometry-based feature and scaffold measurements) diversity assessment tools can be employed to monitor and adjust library development tactics in real time. In summary, metabolomics-driven technologies and simple gene-based specimen barcoding approaches have broad applicability to building chemically diverse natural product libraries.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/mSystems.00644-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2844333-0
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...