Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Högfors-Rönnholm, Eva; Lopez-Fernandez, Margarita; Christel, Stephan; Brambilla, Diego; Huntemann, Marcel; Clum, Alicia; Foster, Brian; Foster, Bryce; Roux, Simon; Palaniappan, Krishnaveni; Varghese, Neha; Mukherjee, Supratim; Reddy, T. B.  K.; Daum, Chris; Copeland, Alex; Chen, I-Min A.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Harmon-Smith, Miranda; Eloe-Fadrosh, Emiley A.; Lundin, Daniel; Engblom, Sten; Dopson, Mark

doi:10.1038/s41597-019-0222-3

Title: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Abstract

Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.

Authors:

^[1]; Lopez-Fernandez, Margarita ^[2]; Christel, Stephan ^[2]; Brambilla, Diego ^[2];

^[3]; Clum, Alicia ^[3]; Foster, Brian ^[3]; Foster, Bryce ^[3];

^[3]; Palaniappan, Krishnaveni ^[3]; Varghese, Neha ^[3];

^[3]; Reddy, T. B. K. ^[3]; Daum, Chris ^[3]; Copeland, Alex ^[3]; Chen, I-Min A. ^[3];

^[3]; Kyrpides, Nikos C. ^[3]; Harmon-Smith, Miranda ^[3];

^[3] more »

Novia Univ. of Applied Sciences, Vaasa (Finland). Research and Development
Linnaeus Univ., Kalmar (Sweden). Centre for Ecology and Evolution in Microbial Model Systems (EEMiS)
Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States)

Publication Date:: Wed Oct 16 00:00:00 EDT 2019

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1572858

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Scientific Data

Additional Journal Information:: Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2052-4463

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 54 ENVIRONMENTAL SCIENCES

Citation Formats


                    Högfors-Rönnholm, Eva, Lopez-Fernandez, Margarita, Christel, Stephan, Brambilla, Diego, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I-Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Harmon-Smith, Miranda, Eloe-Fadrosh, Emiley A., Lundin, Daniel, Engblom, Sten, and Dopson, Mark. Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.  United States: N. p., 2019. 
Web.  doi:10.1038/s41597-019-0222-3.

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                    Högfors-Rönnholm, Eva, Lopez-Fernandez, Margarita, Christel, Stephan, Brambilla, Diego, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I-Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Harmon-Smith, Miranda, Eloe-Fadrosh, Emiley A., Lundin, Daniel, Engblom, Sten, & Dopson, Mark. Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.  United States.  https://doi.org/10.1038/s41597-019-0222-3

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                    Högfors-Rönnholm, Eva, Lopez-Fernandez, Margarita, Christel, Stephan, Brambilla, Diego, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I-Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Harmon-Smith, Miranda, Eloe-Fadrosh, Emiley A., Lundin, Daniel, Engblom, Sten, and Dopson, Mark. Wed .  
"Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials".  United States.  https://doi.org/10.1038/s41597-019-0222-3.  https://www.osti.gov/servlets/purl/1572858.

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@article{osti_1572858,

  title        = {Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials},

  author       = {Högfors-Rönnholm, Eva and Lopez-Fernandez, Margarita and Christel, Stephan and Brambilla, Diego and Huntemann, Marcel and Clum, Alicia and Foster, Brian and Foster, Bryce and Roux, Simon and Palaniappan, Krishnaveni and Varghese, Neha and Mukherjee, Supratim and Reddy, T. B.  K. and Daum, Chris and Copeland, Alex and Chen, I-Min A. and Ivanova, Natalia N. and Kyrpides, Nikos C. and Harmon-Smith, Miranda and Eloe-Fadrosh, Emiley A. and Lundin, Daniel and Engblom, Sten and Dopson, Mark},

  abstractNote = {Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.},

  doi          = {10.1038/s41597-019-0222-3},

  journal      = {Scientific Data},

  number       = 1,

  volume       = 6,

  place        = {United States},

  year         = {Wed Oct 16 00:00:00 EDT 2019},

  month        = {Wed Oct 16 00:00:00 EDT 2019}

}

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Works referenced in this record:

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Högfors-Rönnholm, Eva; Lopez-Fernandez, Margarita; Christel, Stephan
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Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
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Impact of isostatic land uplift and artificial drainage on oxidation of brackish-water sediments rich in metastable iron sulfide
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Iron and sulfur cycling in acid sulfate soil wetlands under dynamic redox conditions: A review
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Boman, Anton; Fröjdö, Sören; Backlund, Krister
Geochimica et Cosmochimica Acta, Vol. 74, Issue 4
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Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
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The ISME Journal, Vol. 5, Issue 10
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Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
dataset, January 2020

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Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
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dataset (3)

Title: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Abstract

Citation Formats

Bacterial Leaching of Metal Sulfides Proceeds by Two Indirect Mechanisms via Thiosulfate or via Polysulfides and Sulfur journal, January 1999

Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials dataset, January 2020

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea journal, April 2011

Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil journal, February 2013

Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms: Sulfur metabolizing acidophiles journal, April 2012

Human Exposure to Metals in Groundwater Affected by Acid Sulfate Soil Disturbance journal, July 2008

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies journal, June 2014

Impact of mitigation strategies on acid sulfate soil chemistry and microbial community journal, September 2015

Impact of mitigation strategies on acid sulfate soil chemistry and microbial community journal, September 2015

Natural sulfur dioxide emissions from sulfuric soils journal, March 2004

Human Exposure to Metals in Groundwater Affected by Acid Sulfate Soil Disturbance journal, July 2008

Impact of isostatic land uplift and artificial drainage on oxidation of brackish-water sediments rich in metastable iron sulfide journal, February 2010

Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil journal, February 2013

Iron and sulfur cycling in acid sulfate soil wetlands under dynamic redox conditions: A review journal, April 2018

Hydrochemical Effects of Surface Liming, Controlled Drainage and Lime-Filter Drainage on Boreal Acid Sulfate Soils journal, August 2006

Natural sulfur dioxide emissions from sulfuric soils journal, March 2004

Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments: Iron oxidation and iron homeostasis in acidophiles journal, November 2011

Impact of isostatic land uplift and artificial drainage on oxidation of brackish-water sediments rich in metastable iron sulfide journal, February 2010

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea journal, April 2011

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities journal, April 2015

Bacterial Leaching of Metal Sulfides Proceeds by Two Indirect Mechanisms via Thiosulfate or via Polysulfides and Sulfur
journal, January 1999

Metadata record for: Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
dataset, January 2020

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
journal, April 2011

Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil
journal, February 2013

Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms: Sulfur metabolizing acidophiles
journal, April 2012

Human Exposure to Metals in Groundwater Affected by Acid Sulfate Soil Disturbance
journal, July 2008

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies
journal, June 2014

Impact of mitigation strategies on acid sulfate soil chemistry and microbial community
journal, September 2015

Impact of mitigation strategies on acid sulfate soil chemistry and microbial community
journal, September 2015

Natural sulfur dioxide emissions from sulfuric soils
journal, March 2004

Human Exposure to Metals in Groundwater Affected by Acid Sulfate Soil Disturbance
journal, July 2008

Impact of isostatic land uplift and artificial drainage on oxidation of brackish-water sediments rich in metastable iron sulfide
journal, February 2010

Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil
journal, February 2013

Iron and sulfur cycling in acid sulfate soil wetlands under dynamic redox conditions: A review
journal, April 2018

Hydrochemical Effects of Surface Liming, Controlled Drainage and Lime-Filter Drainage on Boreal Acid Sulfate Soils
journal, August 2006

Natural sulfur dioxide emissions from sulfuric soils
journal, March 2004

Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments: Iron oxidation and iron homeostasis in acidophiles
journal, November 2011

Impact of isostatic land uplift and artificial drainage on oxidation of brackish-water sediments rich in metastable iron sulfide
journal, February 2010

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
journal, April 2011

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities
journal, April 2015