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Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.

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Title: Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.
Authors: Rodriguez‐R, Luis M.1 (AUTHOR), Tsementzi, Despina1 (AUTHOR), Luo, Chengwei1 (AUTHOR), Konstantinidis, Konstantinos T.1 (AUTHOR) kostas@ce.gatech.edu
Source: Environmental Microbiology. Aug2020, Vol. 22 Issue 8, p3394-3412. 19p.
Subjects: Lakes, Habitat selection, Fresh water, Time series analysis, Microbial communities, Planck (Artificial satellite), Freshwater habitats
Abstract: Summary: Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet‐uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome‐assembled genomes (MAGs) represents >400 yet‐unnamed genomospecies, substantially increasing the number of high‐quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat‐specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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DbLabel: Engineering Source
An: 145204501
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PubTypeId: academicJournal
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  Data: Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.
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  Data: <searchLink fieldCode="AR" term="%22Rodriguez‐R%2C+Luis+M%2E%22">Rodriguez‐R, Luis M.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Tsementzi%2C+Despina%22">Tsementzi, Despina</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Luo%2C+Chengwei%22">Luo, Chengwei</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Konstantinidis%2C+Konstantinos+T%2E%22">Konstantinidis, Konstantinos T.</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> kostas@ce.gatech.edu</i>
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Aug2020, Vol. 22 Issue 8, p3394-3412. 19p.
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  Data: <searchLink fieldCode="DE" term="%22Lakes%22">Lakes</searchLink><br /><searchLink fieldCode="DE" term="%22Habitat+selection%22">Habitat selection</searchLink><br /><searchLink fieldCode="DE" term="%22Fresh+water%22">Fresh water</searchLink><br /><searchLink fieldCode="DE" term="%22Time+series+analysis%22">Time series analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Microbial+communities%22">Microbial communities</searchLink><br /><searchLink fieldCode="DE" term="%22Planck+%28Artificial+satellite%29%22">Planck (Artificial satellite)</searchLink><br /><searchLink fieldCode="DE" term="%22Freshwater+habitats%22">Freshwater habitats</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Summary: Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet‐uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome‐assembled genomes (MAGs) represents >400 yet‐unnamed genomospecies, substantially increasing the number of high‐quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat‐specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
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  Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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        Value: 10.1111/1462-2920.15112
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      – Code: eng
        Text: English
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        PageCount: 19
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      – SubjectFull: Lakes
        Type: general
      – SubjectFull: Habitat selection
        Type: general
      – SubjectFull: Fresh water
        Type: general
      – SubjectFull: Time series analysis
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      – SubjectFull: Microbial communities
        Type: general
      – SubjectFull: Planck (Artificial satellite)
        Type: general
      – SubjectFull: Freshwater habitats
        Type: general
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      – TitleFull: Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.
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            NameFull: Rodriguez‐R, Luis M.
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            NameFull: Luo, Chengwei
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            NameFull: Konstantinidis, Konstantinos T.
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              M: 08
              Text: Aug2020
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              Y: 2020
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