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  • 1
    Online Resource
    Online Resource
    “ Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane
    American Society for Microbiology ; 2020
    In:  mBio Vol. 11, No. 2 ( 2020-04-28)
    Details
    In: mBio, American Society for Microbiology, Vol. 11, No. 2 ( 2020-04-28)
    Abstract: Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, “ Candidatus Ethanoperedens thermophilum” (GoM-Arc1 clade), and its partner bacterium “ Candidatus Desulfofervidus auxilii,” previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of “ Ca. Ethanoperedens,” a sister genus of the recently reported ethane oxidizer “ Candidatus Argoarchaeum.” The metagenome-assembled genome of “ Ca. Ethanoperedens” encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in “ Ca. Ethanoperedens” is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide. IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.00600-20
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 2557172-2
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  • 2
    Online Resource
    Online Resource
    Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems
    American Society for Microbiology ; 2020
    In:  mBio Vol. 11, No. 2 ( 2020-04-28)
    Details
    In: mBio, American Society for Microbiology, Vol. 11, No. 2 ( 2020-04-28)
    Abstract: The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions. IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and—among nitrifiers—unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.03175-19
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 2557172-2
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  • 3
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    Online Resource
    A seagrass harbours a nitrogen-fixing bacterial partner
    Springer Science and Business Media LLC ; 2021
    In:  Nature Vol. 600, No. 7887 ( 2021-12-02), p. 42-43
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 600, No. 7887 ( 2021-12-02), p. 42-43
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/d41586-021-02956-y
    RVK:
    TA 1000
    RVK:
    UA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 4
    Online Resource
    Online Resource
    Unsolved mysteries in marine nitrogen fixation
    Elsevier BV ; 2023
    In:  Trends in Microbiology ( 2023-8)
    Details
    In: Trends in Microbiology, Elsevier BV, ( 2023-8)
    Type of Medium: Online Resource
    ISSN: 0966-842X
    URL: Article
    DOI: 10.1016/j.tim.2023.08.004
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2010995-7
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Nitrification and nitrous oxide dynamics in the Southern California Bight
    Wiley ; 2021
    In:  Limnology and Oceanography Vol. 66, No. 4 ( 2021-04), p. 1099-1112
    Details
    In: Limnology and Oceanography, Wiley, Vol. 66, No. 4 ( 2021-04), p. 1099-1112
    Abstract: The amount of primary production fueled by upwelled “new” nitrate can be used to estimate the amount of organic carbon available for export to the deep ocean. Nitrate production in the euphotic zone from the microbial process of nitrification affects these estimates, yet the controls on nitrification in the upper ocean are debated. This study examines how seasonal cycles in primary production influence rates of nitrification fueled by both ammonia and urea‐derived nitrogen (N), and how these processes relate to the distribution of the greenhouse gas nitrous oxide (N 2 O) using monthly rate measurements from the San Pedro Ocean Time‐series (SPOT) station. Nitrification rates were highest at the onset of upwelling and were correlated with depth‐integrated primary production in the lower euphotic zone. Similar ammonia and urea‐derived N oxidation rates suggest urea is a significant N source fueling nitrification, particularly below the euphotic zone. Nitrification supplied a large proportion of phytoplankton N demand in the lower euphotic zone, implying significant regenerated production. The Southern California Bight was always a source of N 2 O to the atmosphere, which likely was advected into the system from the eastern tropical North Pacific, rather than produced locally from nitrification, and ventilated to the atmosphere during upwelling. Together, the results suggest the coupling of N remineralization and primary production in the upper ocean have important implications for the amount of organic carbon available for export out of the surface ocean, but that transport may dominate over local production in explaining local N 2 O dynamics.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v66.4
    DOI: 10.1002/lno.11667
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2033191-5
    detail.hit.zdb_id: 412737-7
    SSG: 12
    SSG: 14
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  • 6
    Online Resource
    Online Resource
    Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N 2 fixation
    Copernicus GmbH ; 2023
    In:  Earth System Science Data Vol. 15, No. 8 ( 2023-08-15), p. 3673-3709
    Details
    In: Earth System Science Data, Copernicus GmbH, Vol. 15, No. 8 ( 2023-08-15), p. 3673-3709
    Abstract: Abstract. Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).
    Type of Medium: Online Resource
    ISSN: 1866-3516
    URL: Article
    URL: Article
    DOI: 10.5194/essd-15-3673-2023
    DOI: 10.5194/essd-15-3673-2023-supplement
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2023
    detail.hit.zdb_id: 2475469-9
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  • 7
    Online Resource
    Online Resource
    The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes
    American Society for Microbiology ; 2021
    In:  mBio Vol. 12, No. 1 ( 2021-02-23)
    Details
    In: mBio, American Society for Microbiology, Vol. 12, No. 1 ( 2021-02-23)
    Abstract: How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella , a cosmopolitan unicellular eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions. This challenges our usual understanding of chromosomal structure and suggests the possibility of novel mechvanisms in transcriptional regulation. Comprehensive analysis of multiple data sets reveals that Halteria transcription dynamics are influenced by: (i) nonuniform nanochromosome copy numbers correlated with gene-expression level; (ii) dynamic alterations at both the DNA and RNA levels, including alternative internal eliminated sequence (IES) deletions during macronucleus formation and large-scale alternative splicing in transcript maturation; and (iii) extremely short 5′ and 3′ untranslated regions (UTRs) and universal TATA box-like motifs in the compact 5′ subtelomeric regions of most chromosomes. This study broadens the view of ciliate biology and the evolution of unicellular eukaryotes, and identifies Halteria as one of the most compact known eukaryotic genomes, indicating that complex cell structure does not require complex gene architecture.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.01964-20
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2557172-2
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  • 8
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    Online Resource
    The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica
    Oxford University Press (OUP) ; 2020
    In:  FEMS Microbiology Ecology Vol. 96, No. 3 ( 2020-03-01)
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 96, No. 3 ( 2020-03-01)
    Abstract: The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
    Type of Medium: Online Resource
    ISSN: 0168-6496 , 1574-6941
    URL: Article
    DOI: 10.1093/femsec/fiaa010
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1501712-6
    SSG: 12
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  • 9
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    Online Resource
    Publisher Correction: The marine nitrogen cycle: new developments and global change
    Springer Science and Business Media LLC ; 2022
    In:  Nature Reviews Microbiology Vol. 20, No. 7 ( 2022-07), p. 444-444
    Details
    In: Nature Reviews Microbiology, Springer Science and Business Media LLC, Vol. 20, No. 7 ( 2022-07), p. 444-444
    Type of Medium: Online Resource
    ISSN: 1740-1526 , 1740-1534
    URL: Article
    DOI: 10.1038/s41579-022-00752-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2121463-3
    SSG: 12
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  • 10
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    Online Resource
    Nitrification and Nitrous Oxide Production in the Offshore Waters of the Eastern Tropical South Pacific
    American Geophysical Union (AGU) ; 2021
    In:  Global Biogeochemical Cycles Vol. 35, No. 2 ( 2021-02)
    Details
    In: Global Biogeochemical Cycles, American Geophysical Union (AGU), Vol. 35, No. 2 ( 2021-02)
    Abstract: Depth‐integrated ammonia oxidation rates are correlated with sinking particulate nitrogen flux, indicating substrate supply as a primary control of water column nitrification Nitrous oxide is produced from ammonium in the water column, with an instantaneous yield from nitrification lower than previous estimates Higher than anticipated nitrous oxide concentrations were measured in offshore waters, which may arise from local production, leading to large air‐sea fluxes
    Type of Medium: Online Resource
    ISSN: 0886-6236 , 1944-9224
    URL: Article
    DOI: 10.1029/2020GB006716
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2021
    detail.hit.zdb_id: 2021601-4
    SSG: 12
    SSG: 13
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