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Title: Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

Abstract

Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal media (SG only FACs), and the other consortium was treated the same way but received poorly crystalline iron as an additional terminal electron acceptor (SG + Fe FACs). We sequenced the metagenomes of both consortia to a depth of about 150 Mb each, resulting in a coverage of 26× for the more diverse SG + Fe FACs, and 81× for the relatively less diverse SG only FACs. Both consortia were able to quickly grow on switchgrass, and the iron-amended consortium exhibited significantly higher microbial diversity than the unamended consortium. We found evidence of higher stress in the unamended FACs andmore » increased sugar transport and utilization in the ironamended FACs. This work provides metagenomic evidence that supplementation of alternative TEAs may improve feedstock deconstruction in biofuel production.« less

Authors:
 [1];  [2];  [3];  [4];  [3];  [5];  [5];  [5];  [6]
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  1. Univ. of Massachusetts, Amherst, MA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1511358
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 7; Journal Issue: 3; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

De Angelis, Kristen M., D'Haeseleer, Patrik, Chivian, Dylan, Simmons, Blake, Arkin, Adam P., Mavromatis, Konstantinos, Malfatti, Stephanie, Tringe, Susannah, and Hazen, Terry C. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. United States: N. p., 2013. Web. doi:10.4056/sigs.3377516.
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De Angelis, Kristen M., D'Haeseleer, Patrik, Chivian, Dylan, Simmons, Blake, Arkin, Adam P., Mavromatis, Konstantinos, Malfatti, Stephanie, Tringe, Susannah, & Hazen, Terry C. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. United States. https://doi.org/10.4056/sigs.3377516
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De Angelis, Kristen M., D'Haeseleer, Patrik, Chivian, Dylan, Simmons, Blake, Arkin, Adam P., Mavromatis, Konstantinos, Malfatti, Stephanie, Tringe, Susannah, and Hazen, Terry C. Mon . "Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron". United States. https://doi.org/10.4056/sigs.3377516. https://www.osti.gov/servlets/purl/1511358.
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@article{osti_1511358,
title = {Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron},
author = {De Angelis, Kristen M. and D'Haeseleer, Patrik and Chivian, Dylan and Simmons, Blake and Arkin, Adam P. and Mavromatis, Konstantinos and Malfatti, Stephanie and Tringe, Susannah and Hazen, Terry C.},
abstractNote = {Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal media (SG only FACs), and the other consortium was treated the same way but received poorly crystalline iron as an additional terminal electron acceptor (SG + Fe FACs). We sequenced the metagenomes of both consortia to a depth of about 150 Mb each, resulting in a coverage of 26× for the more diverse SG + Fe FACs, and 81× for the relatively less diverse SG only FACs. Both consortia were able to quickly grow on switchgrass, and the iron-amended consortium exhibited significantly higher microbial diversity than the unamended consortium. We found evidence of higher stress in the unamended FACs and increased sugar transport and utilization in the ironamended FACs. This work provides metagenomic evidence that supplementation of alternative TEAs may improve feedstock deconstruction in biofuel production.},
doi = {10.4056/sigs.3377516},
journal = {Standards in Genomic Sciences},
number = 3,
volume = 7,
place = {United States},
year = {Mon Apr 01 00:00:00 EDT 2013},
month = {Mon Apr 01 00:00:00 EDT 2013}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.4056/sigs.3377516
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Cited by: 10 works
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Figures / Tables:

Table 1 Table 1: Classification and general features of the four metagenome data sets according to the Minimum Information about Genomes and Metagenomes (MIMS) standards.
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Works referencing / citing this record:

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient
journal, July 2018

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    Figures / Tables found in this record:

    Table 1 (p. 4)table
    Table 2 (p. 5)table
    Table 3 (p. 7)table
    Table 4 (p. 7)table
    Table 5 (p. 8)table
    Table 6 (p. 10)table
    Figure 1 (p. 11)figure
    Figure 2 (p. 11)figure
    Table 7 Part 1 (p. 12)table
    Figure 3 (p. 13)figure
    Table 7 Part 2 (p. 13)table
    Table 8 (p. 14)table
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