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  • 1
    Publication Date: 2023-03-14
    Description: In this work we used controlled microcosms to study the effect of temperature and pH on brGDGTs in lake water. We collected surface water from Kennedy Lake, Tucson, AZ, a shallow eutrophic artificial reservoir previously described by Martínez-Sosa & Tierney (2019). From the collected samples we set up a series of microcosms, consisting of 1L glass flasks filled with lake water, and manipulated single environmental factors including temperature and pH. For our temperature incubations, we selected four conditions (9C, 18C, 27C and 35C) and incubated 3 1L flasks under each condition for two periods of time (4 or 6 weeks). For the pH incubations, we used commercially available freshwater aquarium non-phosphate buffers (Proprietary composition, Seachem, Madison, GA, USA) to manipulate the pH of the microcosms. For these experiments we targeted four pH conditions (4, 5, 6 and 7), and included two control samples: one where we added enough buffer to maintain the initial pH (Control + Buffer), and another to which we added no buffer (Control - Buffer). GDGTs were analyzed on an Agilent 1260 Infinity HPLC coupled to an Agilent 6120 single quadrupole mass spectrometer using two BEH HILIC silica columns (2.1 x 150 mm, 1.7 um; Waters) and the methodology of Hopmans et al. (2016). We calculated peak areas using the MATLAB package software ORIGAmI (Fleming et al. 2016) and estimated the concentration of brGDGTs by comparing the obtained peaks with a C46 internal standard (Huguet et al. 2006) normalized to the volume of each sample.
    Keywords: Branched glycerol dialkyl glycerol tetraether; Branched glycerol dialkyl glycerol tetraether, Ia; Branched glycerol dialkyl glycerol tetraether, Ib; Branched glycerol dialkyl glycerol tetraether, Ic; Branched glycerol dialkyl glycerol tetraether, IIa; Branched glycerol dialkyl glycerol tetraether, IIa'; Branched glycerol dialkyl glycerol tetraether, IIb; Branched glycerol dialkyl glycerol tetraether, IIb'; Branched glycerol dialkyl glycerol tetraether, IIIa; Branched glycerol dialkyl glycerol tetraether, IIIa'; brGDGTs; Calculated; Cyclization ratio of branched tetraethers; Degree of cyclisation; Experiment; Incubation duration; Isomer ratio; Kennedy_Lake_water_microcosm; Laboratory experiment; lakes; Methylation index of 5-methyl branched glycerol dialkyl glycerol tetraether; microcosms; pH; Sample ID; Standard deviation; Temperature; Temperature, water; Tucson, Arizona, USA
    Type: Dataset
    Format: text/tab-separated-values, 528 data points
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  • 2
    Publication Date: 2024-02-07
    Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
    Type: Article , PeerReviewed
    Format: text
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  • 3
    Publication Date: 2021-12-01
    Print ISSN: 0048-9697
    Electronic ISSN: 1879-1026
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Elsevier
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