1
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Duchesneau K, Defrenne CE, Petro C, Malhotra A, Moore JAM, Childs J, Hanson PJ, Iversen CM, Kostka JE. Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO 2 in northern peatlands. New Phytol 2024; 242:1333-1347. [PMID: 38515239 DOI: 10.1111/nph.19690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024]
Abstract
Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.
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Affiliation(s)
- Katherine Duchesneau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Camille E Defrenne
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Caitlin Petro
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Avni Malhotra
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jessica A M Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joanne Childs
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Paul J Hanson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Colleen M Iversen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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2
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Rolando JL, Kolton M, Song T, Liu Y, Pinamang P, Conrad R, Morris JT, Konstantinidis KT, Kostka JE. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora. Nat Commun 2024; 15:3607. [PMID: 38684658 PMCID: PMC11059160 DOI: 10.1038/s41467-024-47646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.
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Affiliation(s)
- J L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - M Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - T Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Y Liu
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- The Pennsylvania State University, Department of Civil & Environmental Engineering, University Park, PA, 16802, USA
| | - P Pinamang
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - R Conrad
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - J T Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, 29201, USA
| | - K T Konstantinidis
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | - J E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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3
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy. Sci Rep 2024; 14:5812. [PMID: 38461279 PMCID: PMC10925023 DOI: 10.1038/s41598-024-56443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Madison Green
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Abigail Diering
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marcus T Cicerone
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Francisco E Robles
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30318, USA.
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4
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Berg G, Dorador C, Egamberdieva D, Kostka JE, Ryu CM, Wassermann B. Shared governance in the plant holobiont and implications for one health. FEMS Microbiol Ecol 2024; 100:fiae004. [PMID: 38364305 PMCID: PMC10876113 DOI: 10.1093/femsec/fiae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Angamos 601, Antofagasta, Chile
| | - Dilfuza Egamberdieva
- Institute of Fundamental and Applied Research, National Research University, TIIAME, Kari Niyazi street 39, Tashkent 100000, Uzbekistan
- Medical School, Central Asian University, Milliy bog street 264, Tashkent 111221, Uzbekistan
| | - Joel E Kostka
- Schools of Biological Sciences and Earth & Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, United States
| | - Choong-Min Ryu
- Biosystems and Bioengineering, University of Science and Technology KRIBB School, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
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5
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Ofiti NOE, Schmidt MWI, Abiven S, Hanson PJ, Iversen CM, Wilson RM, Kostka JE, Wiesenberg GLB, Malhotra A. Climate warming and elevated CO 2 alter peatland soil carbon sources and stability. Nat Commun 2023; 14:7533. [PMID: 37985767 PMCID: PMC10662476 DOI: 10.1038/s41467-023-43410-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and elevated atmospheric CO2 concentration (eCO2) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO2 increased plant-derived SOC compounds. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and eCO2. The decline in SOC compounds with warming and gains from new root-derived C under eCO2, suggest that warming and eCO2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.
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Affiliation(s)
- Nicholas O E Ofiti
- Department of Geography, University of Zurich, Zurich, Switzerland.
- CEREEP-Ecotron Ile De France, ENS, CNRS, PSL Research University, Saint-Pierre-lès-Nemours, France.
| | | | - Samuel Abiven
- CEREEP-Ecotron Ile De France, ENS, CNRS, PSL Research University, Saint-Pierre-lès-Nemours, France
- Laboratoire de Géologie, Département de Géosciences, Ecole normale supérieure (ENS), Paris, France
| | - Paul J Hanson
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Avni Malhotra
- Department of Geography, University of Zurich, Zurich, Switzerland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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6
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-Free Functional Analysis of Root-Associated Microbes with Dynamic Quantitative Oblique Back-illumination Microscopy. Res Sq 2023:rs.3.rs-3517586. [PMID: 37961396 PMCID: PMC10635382 DOI: 10.21203/rs.3.rs-3517586/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over five days, we observed increased dynamic activity in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize bacterial activity within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial activity and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- Georgia Institute of Technology, George W. Woodruff School of Mechanical Engineering, Atlanta, GA, 30318, USA
| | - Madison Green
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Abigail Diering
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Marcus T. Cicerone
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Lily S. Cheung
- Georgia Institute of Technology, School of Chemical and Biomolecular Engineering, Atlanta, GA, 30332, USA
| | - Joel E. Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Francisco E. Robles
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, GA, 30318, USA
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7
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Song T, Liu Y, Kolton M, Wilson RM, Keller JK, Rolando JL, Chanton JP, Kostka JE. Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog. FEMS Microbiol Ecol 2023; 99:fiad060. [PMID: 37280172 DOI: 10.1093/femsec/fiad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023] Open
Abstract
Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.
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Affiliation(s)
- Tianze Song
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Yutong Liu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- Department of Civil & Environmental Engineering, Pennsylvania State University, University Park, University Park, PA 16802, United States
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, 8499000, Israel
| | - Rachel M Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Jason K Keller
- Schmid College of Science and Technology, Chapman University, 1 University Dr, Orange, CA 92866, United States
| | - Jose L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jeffrey P Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30318, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
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8
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Petro C, Carrell AA, Wilson RM, Duchesneau K, Noble-Kuchera S, Song T, Iversen CM, Childs J, Schwaner G, Chanton JP, Norby RJ, Hanson PJ, Glass JB, Weston DJ, Kostka JE. Climate drivers alter nitrogen availability in surface peat and decouple N 2 fixation from CH 4 oxidation in the Sphagnum moss microbiome. Glob Chang Biol 2023; 29:3159-3176. [PMID: 36999440 DOI: 10.1111/gcb.16651] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N2 -fixing (diazotrophic) and CH4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH4 , CO2 ) and nitrogen (NH4 -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO2 . Under ambient CO2 , warming increased plant-available NH4 -N in surface peat, excess N accumulated in Sphagnum tissue, and N2 fixation activity decreased. Elevated CO2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.
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Affiliation(s)
- Caitlin Petro
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Katherine Duchesneau
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sekou Noble-Kuchera
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tianze Song
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Colleen M Iversen
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joanne Childs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Geoff Schwaner
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jeffrey P Chanton
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Richard J Norby
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Paul J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joel E Kostka
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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9
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. Microbiome 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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10
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Ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Correction to: Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 2022; 10:17. [PMID: 35078529 PMCID: PMC8790829 DOI: 10.1186/s40168-022-01229-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
| | | | - Jackson W Sorensen
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Laura A Zinke
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Rachel M Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Eric R Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Paul J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeffrey P Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | | | - Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California Davis, Davis, CA, USA.
- Genome Center, University of California Davis, Davis, CA, USA.
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11
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Ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Correction to: Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 2021; 9:242. [PMID: 34911559 PMCID: PMC8672481 DOI: 10.1186/s40168-021-01210-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
| | | | | | - Laura A Zinke
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Rachel M Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Eric R Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Paul J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeffrey P Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | | | - Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
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12
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Karthikeyan S, Hatt JK, Kim M, Spain JC, Huettel M, Kostka JE, Konstantinidis KT. A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation. Environ Microbiol Rep 2021; 13:830-840. [PMID: 34672103 DOI: 10.1111/1758-2229.13018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Alkanes are ubiquitous in marine ecosystems and originate from diverse sources ranging from natural oil seeps to anthropogenic inputs and biogenic production by cyanobacteria. Enzymes that degrade cyanobacterial alkanes (typically C15-C17 compounds) such as the alkane monooxygenase (AlkB) are widespread, but it remains unclear whether or not AlkB variants exist that specialize in degradation of crude oil from natural or accidental spills, a much more complex mixture of long-chain hydrocarbons. In the present study, large-scale analysis of available metagenomic and genomic data from the Gulf of Mexico (GoM) oil spill revealed a novel, divergent AlkB clade recovered from genomes with no cultured representatives that was dramatically increased in abundance in crude-oil impacted ecosystems. In contrast, the AlkB clades associated with biotransformation of cyanobacterial alkanes belonged to 'canonical' or hydrocarbonoclastic clades, and based on metatranscriptomics data and compared to the novel clade, were much more weakly expressed during crude oil biodegradation in laboratory mesocosms. The absence of this divergent AlkB clade in metagenomes of uncontaminated samples from the global ocean survey but not from the GoM as well as its frequent horizontal gene transfer indicated a priming effect of the Gulf for crude oil biodegradation likely driven by natural oil seeps.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Minjae Kim
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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13
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ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
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Affiliation(s)
| | | | - Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Rachel M. Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | | | - Joel E. Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
- Genome Center, University of California, Davis, Davis, CA USA
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14
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Heritier-Robbins P, Karthikeyan S, Hatt JK, Kim M, Huettel M, Kostka JE, Konstantinidis KT, Rodriguez-R LM. Beach sand oil spills select for generalist microbial populations. ISME J 2021; 15:3418-3422. [PMID: 34088976 PMCID: PMC8528907 DOI: 10.1038/s41396-021-01017-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 11/15/2022]
Abstract
The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations (e.g., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.
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Affiliation(s)
- Patrick Heritier-Robbins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria.
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15
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Salmon VG, Brice DJ, Bridgham S, Childs J, Graham J, Griffiths NA, Hofmockel K, Iversen CM, Jicha TM, Kolka RK, Kostka JE, Malhotra A, Norby RJ, Phillips JR, Ricciuto D, Schadt CW, Sebestyen SD, Shi X, Walker AP, Warren JM, Weston DJ, Yang X, Hanson PJ. Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change. Plant Soil 2021; 466:649-674. [PMID: 36267144 PMCID: PMC9580354 DOI: 10.1007/s11104-021-05065-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/23/2021] [Indexed: 06/16/2023]
Abstract
AIMS Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA. METHODS N and P within plants, soils, and water are quantified based on field measurements. The resulting empirical dataset are then compared to modern-day, site-level simulations from the peatland land surface version of the Energy Exascale Earth System Model (ELM-SPRUCE). RESULTS Our results reveal N is accumulating in the ecosystem at 0.2 ± 0.1 g N m-2 year-1 but annual P inputs to this ecosystem are balanced by losses. Biomass stoichiometry indicates that plant functional types differ in N versus P limitation, with trees exhibiting a stronger N limitation than ericaceous shrubs or Sphagnum moss. High biomass and productivity of Sphagnum results in the moss layer storing and cycling a large proportion of plant N and P. Comparing our empirically-derived nutrient budgets to ELM-SPRUCE shows the model captures N cycling within dominant plant functional types well. CONCLUSIONS The nutrient budgets and stoichiometry presented serve as a baseline for quantifying the nutrient cycling response of peatland ecosystems to both observed and simulated climate change. Our analysis improves our understanding of N and P dynamics within nutrient-limited peatlands and represents a crucial step toward improving C-cycle projections into the twenty-first century.
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Affiliation(s)
- Verity G Salmon
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Deanne J Brice
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Joanne Childs
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jake Graham
- Department of Geosciences, Boise State University, Boise, ID, USA
| | - Natalie A Griffiths
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kirsten Hofmockel
- Earth and Biological Sciences Directorate Molecular, Science Laboratory, Pacific Northwest National, Laboratory, Richland, WA, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Colleen M Iversen
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Terri M Jicha
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Laboratory, Mid-Continent Ecology Division, Center for Computational Toxicology and Exposure, Great, Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Randy K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, MN, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Avni Malhotra
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Richard J Norby
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Jana R Phillips
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel Ricciuto
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Christopher W Schadt
- Climate Change Science Institute and Biosciences, Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Xiaoying Shi
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Anthony P Walker
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeffrey M Warren
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David J Weston
- Climate Change Science Institute and Biosciences, Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaojuan Yang
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul J Hanson
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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16
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Medina-Cordoba LK, Chande AT, Rishishwar L, Mayer LW, Valderrama-Aguirre LC, Valderrama-Aguirre A, Gaby JC, Kostka JE, Jordan IK. Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Sci Rep 2021; 11:9187. [PMID: 33911103 PMCID: PMC8080613 DOI: 10.1038/s41598-021-88380-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/07/2021] [Indexed: 01/26/2023] Open
Abstract
Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.
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Affiliation(s)
- Luz K Medina-Cordoba
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Leonard W Mayer
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lina C Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, INCAUCA S.A.S., Cali, Valle del Cauca, Colombia
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Universidad Santiago de Cali, Cali, Colombia
| | - John Christian Gaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Dr NW, Atlanta, GA, 30332, USA.
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,Applied Bioinformatics Laboratory, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332, USA.
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17
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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18
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Karthikeyan S, Kim M, Heritier-Robbins P, Hatt JK, Spain JC, Overholt WA, Huettel M, Kostka JE, Konstantinidis KT. Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles. Environ Sci Technol 2020; 54:10088-10099. [PMID: 32667785 DOI: 10.1021/acs.est.0c02834] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Minjae Kim
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Patrick Heritier-Robbins
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Janet K Hatt
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, 11000 University Parkway, Pensacola 32514, Florida, United States
| | - Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee 32306-4320, Florida, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Konstantinos T Konstantinidis
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
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19
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Karthikeyan S, Rodriguez-R LM, Heritier-Robbins P, Hatt JK, Huettel M, Kostka JE, Konstantinidis KT. Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes. Environ Microbiol 2020; 22:2094-2106. [PMID: 32114693 DOI: 10.1111/1462-2920.14966] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022]
Abstract
Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.
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Affiliation(s)
- Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Patrick Heritier-Robbins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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20
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Hackbusch S, Noirungsee N, Viamonte J, Sun X, Bubenheim P, Kostka JE, Müller R, Liese A. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico. Mar Pollut Bull 2020; 150:110683. [PMID: 31753565 DOI: 10.1016/j.marpolbul.2019.110683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.
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Affiliation(s)
- Steffen Hackbusch
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Nuttapol Noirungsee
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Juan Viamonte
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Xiaoxu Sun
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Paul Bubenheim
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Joel E Kostka
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
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21
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Shin B, Bociu I, Kolton M, Huettel M, Kostka JE. Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach. Sci Rep 2019; 9:19401. [PMID: 31852991 PMCID: PMC6920467 DOI: 10.1038/s41598-019-55625-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ioana Bociu
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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22
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Sun X, Chu L, Mercando E, Romero I, Hollander D, Kostka JE. Dispersant Enhances Hydrocarbon Degradation and Alters the Structure of Metabolically Active Microbial Communities in Shallow Seawater From the Northeastern Gulf of Mexico. Front Microbiol 2019; 10:2387. [PMID: 31749769 PMCID: PMC6842959 DOI: 10.3389/fmicb.2019.02387] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 10/01/2019] [Indexed: 01/23/2023] Open
Abstract
Dispersant application is a primary emergency oil spill response strategy and yet the efficacy and unintended consequences of this approach in marine ecosystems remain controversial. To address these uncertainties, ex situ incubations were conducted to quantify the impact of dispersant on petroleum hydrocarbon (PHC) biodegradation rates and microbial community structure at as close as realistically possible to approximated in situ conditions [2 ppm v/v oil with or without dispersant, at a dispersant to oil ratio (DOR) of 1:15] in surface seawater. Biodegradation rates were not substantially affected by dispersant application at low mixing conditions, while under completely dispersed conditions, biodegradation was substantially enhanced, decreasing the overall half-life of total PHC compounds from 15.4 to 8.8 days. While microbial respiration and growth were not substantially altered by dispersant treatment, RNA analysis revealed that dispersant application resulted in pronounced changes to the composition of metabolically active microbial communities, and the abundance of nitrogen-fixing prokaryotes, as determined by qPCR of nitrogenase (nifH) genes, showed a large increase. While the Gammaproteobacteria were enriched in all treatments, the Betaproteobacteria and different families of Alphaproteobacteria predominated in the oil and dispersant treatment, respectively. Results show that mixing conditions regulate the efficacy of dispersant application in an oil slick, and the quantitative increase in the nitrogen-fixing microbial community indicates a selection pressure for nitrogen fixation in response to a readily biodegradable, nitrogen-poor substrate.
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Affiliation(s)
- Xiaoxu Sun
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science and Technology, Guangzhou, China
| | - Lena Chu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Elisa Mercando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Isabel Romero
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
| | - David Hollander
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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23
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Overholt WA, Schwing P, Raz KM, Hastings D, Hollander DJ, Kostka JE. The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills. Environ Microbiol 2019; 21:4316-4329. [PMID: 31469487 DOI: 10.1111/1462-2920.14794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/20/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.
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Affiliation(s)
- Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick Schwing
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Kala M Raz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Hastings
- Department of Marine Science, Eckerd College, St. Petersburg, FL, USA
| | - David J Hollander
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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24
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Carrell AA, Kolton M, Glass JB, Pelletier DA, Warren MJ, Kostka JE, Iversen CM, Hanson PJ, Weston DJ. Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss (Sphagnum fallax) microbiomes. Glob Chang Biol 2019; 25:2993-3004. [PMID: 31148286 PMCID: PMC6852288 DOI: 10.1111/gcb.14715] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 05/19/2023]
Abstract
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.
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Affiliation(s)
- Alyssa A. Carrell
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Max Kolton
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | | | - Melissa J. Warren
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
- Present address:
CH2MAtlantaGeorgia30328USA
| | - Joel E. Kostka
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | - Colleen M. Iversen
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - David J. Weston
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
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25
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Kolton M, Marks A, Wilson RM, Chanton JP, Kostka JE. Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States). Front Microbiol 2019; 10:870. [PMID: 31105668 PMCID: PMC6498409 DOI: 10.3389/fmicb.2019.00870] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 11/17/2022] Open
Abstract
Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.
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Affiliation(s)
- Max Kolton
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ansley Marks
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Rachel M. Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Jeffrey P. Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Joel E. Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
- School of Earth and Atmospheric Science, Georgia Institute of Technology, Atlanta, GA, United States
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26
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Huettel M, Overholt WA, Kostka JE, Hagan C, Kaba J, Wells WB, Dudley S. Corrigendum to "Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping" [Mar. Pollut. Bull. 126 (2018) 488-500]. Mar Pollut Bull 2018; 133:943. [PMID: 29910141 DOI: 10.1016/j.marpolbul.2018.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Markus Huettel
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States of America.
| | - Will A Overholt
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States of America
| | - Joel E Kostka
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States of America.
| | - Christopher Hagan
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States of America.
| | - John Kaba
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States of America
| | - Wm Brian Wells
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States of America.
| | - Stacia Dudley
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States of America.
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27
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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28
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Huettel M, Overholt WA, Kostka JE, Hagan C, Kaba J, Wells WB, Dudley S. Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping. Mar Pollut Bull 2018; 126:488-500. [PMID: 29421130 DOI: 10.1016/j.marpolbul.2017.10.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 09/25/2017] [Accepted: 10/21/2017] [Indexed: 06/08/2023]
Abstract
After Deepwater Horizon oil reached the Florida coast, oil was buried in Pensacola Beach (PB) sands to ~70cm depth, resulting in Total Petroleum Hydrocarbon (TPH) concentrations up to ~2kg per meter of beach. This study followed the decomposition of the buried oil and the factors influencing its degradation. The abundance of bacteria in oiled sand increased by 2 orders of magnitude within one week after oil burial, while diversity decreased by ~50%. Half-lives of aliphatic and aromatic hydrocarbons reached 25 and 22days, respectively. Aerobic microbial oil decomposition, promoted by tidal pumping, and human cleaning activities effectively removed oil from the beach. After one year, concentrations of GC-amenable hydrocarbons at PB were similar to those in the uncontaminated reference beach at St. George Island/FL, and microbial populations that disappeared after the oil contamination had reestablished. Yet, oxihydrocarbons can be found at PB to the present day.
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Affiliation(s)
- Markus Huettel
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Will A Overholt
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States.
| | - Joel E Kostka
- Georgia Institute of Technology, Schools of Biology and Earth & Atmospheric Sciences, 310 Ferst Drive, Atlanta, GA 30332-0230, United States.
| | - Christopher Hagan
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - John Kaba
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Wm Brian Wells
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
| | - Stacia Dudley
- Florida State University, Department of Earth, Ocean and Atmospheric Science, 117 N Woodward Ave., Tallahassee, FL 32306, United States.
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29
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Weston DJ, Turetsky MR, Johnson MG, Granath G, Lindo Z, Belyea LR, Rice SK, Hanson DT, Engelhardt KAM, Schmutz J, Dorrepaal E, Euskirchen ES, Stenøien HK, Szövényi P, Jackson M, Piatkowski BT, Muchero W, Norby RJ, Kostka JE, Glass JB, Rydin H, Limpens J, Tuittila ES, Ullrich KK, Carrell A, Benscoter BW, Chen JG, Oke TA, Nilsson MB, Ranjan P, Jacobson D, Lilleskov EA, Clymo RS, Shaw AJ. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytol 2018; 217:16-25. [PMID: 29076547 DOI: 10.1111/nph.14860] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Merritt R Turetsky
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79414, USA
| | - Gustaf Granath
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-750 07, Uppsala, Sweden
| | - Zoë Lindo
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lisa R Belyea
- School of Geography, Queen Mary University of London, London, E1 4NS, UK
| | - Steven K Rice
- Department of Biological Sciences, Union College, Schenectady, NY, 12308, USA
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Katharina A M Engelhardt
- Appalachian Lab, University of Maryland Center of Environmental Science, Frostburg, MD, 21532, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Ellen Dorrepaal
- Climate Impacts Research Center, Department of Ecology and Environmental Science, Umeå University, 98107, Abisko, Sweden
| | | | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | | | | | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Norby
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jennifer B Glass
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Håkan Rydin
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Juul Limpens
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University, Droevendaalse steeg 3a, NL-6708 PD, Wageningen, the Netherlands
| | - Eeva-Stiina Tuittila
- Peatland and Soil Ecology Group, School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | | | - Alyssa Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brian W Benscoter
- Department of Biological Sciences, Florida Atlantic University, Davie, FL, 33314, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Tobi A Oke
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mats B Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE-901 83, Umeå, Sweden
| | - Priya Ranjan
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996-4561, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Erik A Lilleskov
- US Forest Service, Northern Research Station, 410 MacInnes Dr., Houghton, MI, 49931, USA
| | - R S Clymo
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
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Kwon MJ, Beulig F, Ilie I, Wildner M, Küsel K, Merbold L, Mahecha MD, Zimov N, Zimov SA, Heimann M, Schuur EAG, Kostka JE, Kolle O, Hilke I, Göckede M. Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain. Glob Chang Biol 2017; 23:2396-2412. [PMID: 27901306 DOI: 10.1111/gcb.13558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 05/06/2023]
Abstract
As surface temperatures are expected to rise in the future, ice-rich permafrost may thaw, altering soil topography and hydrology and creating a mosaic of wet and dry soil surfaces in the Arctic. Arctic wetlands are large sources of CH4 , and investigating effects of soil hydrology on CH4 fluxes is of great importance for predicting ecosystem feedback in response to climate change. In this study, we investigate how a decade-long drying manipulation on an Arctic floodplain influences CH4 -associated microorganisms, soil thermal regimes, and plant communities. Moreover, we examine how these drainage-induced changes may then modify CH4 fluxes in the growing and nongrowing seasons. This study shows that drainage substantially lowered the abundance of methanogens along with methanotrophic bacteria, which may have reduced CH4 cycling. Soil temperatures of the drained areas were lower in deep, anoxic soil layers (below 30 cm), but higher in oxic topsoil layers (0-15 cm) compared to the control wet areas. This pattern of soil temperatures may have reduced the rates of methanogenesis while elevating those of CH4 oxidation, thereby decreasing net CH4 fluxes. The abundance of Eriophorum angustifolium, an aerenchymatous plant species, diminished significantly in the drained areas. Due to this decrease, a higher fraction of CH4 was alternatively emitted to the atmosphere by diffusion, possibly increasing the potential for CH4 oxidation and leading to a decrease in net CH4 fluxes compared to a control site. Drainage lowered CH4 fluxes by a factor of 20 during the growing season, with postdrainage changes in microbial communities, soil temperatures, and plant communities also contributing to this reduction. In contrast, we observed CH4 emissions increased by 10% in the drained areas during the nongrowing season, although this difference was insignificant given the small magnitudes of fluxes. This study showed that long-term drainage considerably reduced CH4 fluxes through modified ecosystem properties.
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Affiliation(s)
- Min Jung Kwon
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Felix Beulig
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburgerstr 159, 07743 Jena, Germany
| | - Iulia Ilie
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Marcus Wildner
- Geoecology-Environmental Science: Micrometeorology and Atmospheric Chemistry, Faculty of Biology, Chemistry and Earth Science, University of Bayreuth, Universitätsstr 30, 95447 Bayreuth, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburgerstr 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5d, 04103, Leipzig, Germany
| | - Lutz Merbold
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Universitätstr 16, 8092 Zürich, Switzerland
| | - Miguel D Mahecha
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5d, 04103, Leipzig, Germany
| | - Nikita Zimov
- North-East Science Station, Pacific Institute for Geography, Far-Eastern Branch of Russian Academy of Science, PO Box 18, Cherskii, Republic of Sakha (Yakutia), Russia
| | - Sergey A Zimov
- North-East Science Station, Pacific Institute for Geography, Far-Eastern Branch of Russian Academy of Science, PO Box 18, Cherskii, Republic of Sakha (Yakutia), Russia
| | - Martin Heimann
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
- Division of Atmospheric Sciences, Department of Physics, PO Box 64, FI-00014 University of Helsinki, Helsinki, Finland
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, PO Box 5620, Flagstaff, AZ 86011, USA
| | - Joel E Kostka
- School of Biology, Georgia Institute of Technology, North Avenue, Atlanta, GA 30332, USA
| | - Olaf Kolle
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Mathias Göckede
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
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Kostka JE, Weston DJ, Glass JB, Lilleskov EA, Shaw AJ, Turetsky MR. The Sphagnum microbiome: new insights from an ancient plant lineage. New Phytol 2016; 211:57-64. [PMID: 27173909 DOI: 10.1111/nph.13993] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/15/2016] [Indexed: 05/03/2023]
Abstract
57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.
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Affiliation(s)
- Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN, 37831, USA
| | - Jennifer B Glass
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Erik A Lilleskov
- Northern Research Station, USDA Forest Service, Houghton, MI, 49931, USA
| | | | - Merritt R Turetsky
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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32
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Brooks GR, Larson RA, Schwing PT, Romero I, Moore C, Reichart GJ, Jilbert T, Chanton JP, Hastings DW, Overholt WA, Marks KP, Kostka JE, Holmes CW, Hollander D. Sedimentation Pulse in the NE Gulf of Mexico following the 2010 DWH Blowout. PLoS One 2015; 10:e0132341. [PMID: 26172639 PMCID: PMC4501746 DOI: 10.1371/journal.pone.0132341] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/12/2015] [Indexed: 02/01/2023] Open
Abstract
The objective of this study was to investigate the impacts of the Deepwater Horizon (DWH) oil discharge at the seafloor as recorded in bottom sediments of the DeSoto Canyon region in the northeastern Gulf of Mexico. Through a close coupling of sedimentological, geochemical, and biological approaches, multiple independent lines of evidence from 11 sites sampled in November/December 2010 revealed that the upper ~1 cm depth interval is distinct from underlying sediments and results indicate that particles originated at the sea surface. Consistent dissimilarities in grain size over the surficial ~1 cm of sediments correspond to excess 234Th depths, which indicates a lack of vertical mixing (bioturbation), suggesting the entire layer was deposited within a 4–5 month period. Further, a time series from four deep-sea sites sampled up to three additional times over the following two years revealed that excess 234Th depths, accumulation rates, and 234Th inventories decreased rapidly, within a few to several months after initial coring. The interpretation of a rapid sedimentation pulse is corroborated by stratification in solid phase Mn, which is linked to diagenesis and redox change, and the dramatic decrease in benthic formanifera density that was recorded in surficial sediments. Results are consistent with a brief depositional pulse that was also reported in previous studies of sediments, and marine snow formation in surface waters closer to the wellhead during the summer and fall of 2010. Although sediment input from the Mississippi River and advective transport may influence sedimentation on the seafloor in the DeSoto Canyon region, we conclude based on multidisciplinary evidence that the sedimentation pulse in late 2010 is the product of marine snow formation and is likely linked to the DWH discharge.
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Affiliation(s)
- Gregg R. Brooks
- Department of Marine Science, Eckerd College, Saint Petersburg, FL, United States of America
- * E-mail: (GB)
| | - Rebekka A. Larson
- Department of Marine Science, Eckerd College, Saint Petersburg, FL, United States of America
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
| | - Patrick T. Schwing
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
| | - Isabel Romero
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
| | - Christopher Moore
- Department of Marine Science, Eckerd College, Saint Petersburg, FL, United States of America
| | - Gert-Jan Reichart
- Department of Earth Science, Utrecht University, Utrecht, The Netherlands
- Marine Geology Department, Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Tom Jilbert
- Department of Earth Science, Utrecht University, Utrecht, The Netherlands
| | - Jeff P. Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States of America
| | - David W. Hastings
- Department of Marine Science, Eckerd College, Saint Petersburg, FL, United States of America
| | - Will A. Overholt
- Schools of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332–0230, United States of America
| | - Kala P. Marks
- Schools of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332–0230, United States of America
| | - Joel E. Kostka
- Schools of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332–0230, United States of America
- Schools of Earth & Atmospheric Sciences, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia, 30332–0230, United States of America
| | - Charles W. Holmes
- Environchron, 9103 64th Ave. E., Bradenton, FL, United States of America
| | - David Hollander
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
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33
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Lin X, Handley KM, Gilbert JA, Kostka JE. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J 2015; 9:2740-4. [PMID: 26000553 DOI: 10.1038/ismej.2015.77] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/28/2015] [Accepted: 04/01/2015] [Indexed: 01/08/2023]
Abstract
To probe the metabolic potential of abundant Archaea in boreal peats, we reconstructed two near-complete archaeal genomes, affiliated with Thaumarchaeota group 1.1c (bin Fn1, 8% abundance), which was a genomically unrepresented group, and Thermoplasmata (bin Bg1, 26% abundance), from metagenomic data acquired from deep anoxic peat layers. Each of the near-complete genomes encodes the potential to degrade long-chain fatty acids (LCFA) via β-oxidation. Fn1 has the potential to oxidize LCFA either by syntrophic interaction with methanogens or by coupling oxidation with anaerobic respiration using fumarate as a terminal electron acceptor (TEA). Fn1 is the first Thaumarchaeota genome without an identifiable carbon fixation pathway, indicating that this mesophilic phylum encompasses more diverse metabolisms than previously thought. Furthermore, we report genetic evidence suggestive of sulfite and/or organosulfonate reduction by Thermoplasmata Bg1. In deep peat, inorganic TEAs are often depleted to extremely low levels, yet the anaerobic respiration predicted for two abundant archaeal members suggests organic electron acceptors such as fumarate and organosulfonate (enriched in humic substances) may be important for respiration and C mineralization in peatlands.
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Affiliation(s)
- Xueju Lin
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, Biosciences Division,Argonne National Laboratory, Lemont, IL, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, Biosciences Division,Argonne National Laboratory, Lemont, IL, USA.,Marine Biological Laboratory, Woods Hole, MA, USA.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Joel E Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME J 2015; 9:1928-40. [PMID: 25689026 DOI: 10.1038/ismej.2015.5] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/16/2014] [Accepted: 12/23/2014] [Indexed: 12/30/2022]
Abstract
Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.
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Affiliation(s)
| | - Will A Overholt
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Christopher Hagan
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA, USA [2] School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- 1] School of Biology, Georgia Institute of Technology, Atlanta, GA, USA [2] School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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Abstract
The Deepwater Horizon oil spill in the northern Gulf of Mexico represents the largest marine accidental oil spill in history. It is distinguished from past spills in that it occurred at the greatest depth (1,500 m), the amount of hydrocarbon gas (mostly methane) lost was equivalent to the mass of crude oil released, and dispersants were used for the first time in the deep sea in an attempt to remediate the spill. The spill is also unique in that it has been characterized with an unprecedented level of resolution using next-generation sequencing technologies, especially for the ubiquitous hydrocarbon-degrading microbial communities that appeared largely to consume the gases and to degrade a significant fraction of the petroleum. Results have shown an unexpectedly rapid response of deep-sea Gammaproteobacteria to oil and gas and documented a distinct succession correlated with the control of the oil flow and well shut-in. Similar successional events, also involving Gammaproteobacteria, have been observed in nearshore systems as well.
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Affiliation(s)
- G M King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803;
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36
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Canion A, Overholt WA, Kostka JE, Huettel M, Lavik G, Kuypers MMM. Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments. Environ Microbiol 2014; 16:3331-44. [DOI: 10.1111/1462-2920.12593] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 08/03/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Andy Canion
- Earth, Ocean, and Atmospheric Science Department; Florida State University; Tallahassee FL USA
| | - Will A. Overholt
- Schools of Biology and Earth and Atmospheric Science; Georgia Institute of Technology; Atlanta GA USA
| | - Joel E. Kostka
- Schools of Biology and Earth and Atmospheric Science; Georgia Institute of Technology; Atlanta GA USA
| | - Markus Huettel
- Earth, Ocean, and Atmospheric Science Department; Florida State University; Tallahassee FL USA
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology; Bremen Germany
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37
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Kostka JE, Teske AP, Joye SB, Head IM. The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems. Front Microbiol 2014; 5:471. [PMID: 25237309 PMCID: PMC4154464 DOI: 10.3389/fmicb.2014.00471] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022] Open
Affiliation(s)
- Joel E Kostka
- School of Biology and Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina Chapel Hill, NC, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia Athens, GA, USA
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
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39
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Abstract
The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter.
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Affiliation(s)
- Markus Huettel
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida 32306-4320;
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40
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Canion A, Prakash O, Green SJ, Jahnke L, Kuypers MMM, Kostka JE. Isolation and physiological characterization of psychrophilic denitrifying bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway). Environ Microbiol 2013; 15:1606-18. [DOI: 10.1111/1462-2920.12110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/01/2013] [Accepted: 02/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Andy Canion
- Earth Ocean and Atmospheric Science Department; Florida State University; Tallahassee; FL; USA
| | - Om Prakash
- Earth Ocean and Atmospheric Science Department; Florida State University; Tallahassee; FL; USA
| | | | - Linda Jahnke
- NASA Astrobiology Institute; Ames Research Center; Moffett Field; CA; USA
| | | | - Joel E. Kostka
- School of Biology; Georgia Institute of Technology; Atlanta; GA; USA
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41
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Gray SM, Akob DM, Green SJ, Kostka JE. The bacterial composition within the Sarracenia purpurea model system: local scale differences and the relationship with the other members of the food web. PLoS One 2012; 7:e50969. [PMID: 23227224 PMCID: PMC3515446 DOI: 10.1371/journal.pone.0050969] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/29/2012] [Indexed: 02/01/2023] Open
Abstract
The leaves of the carnivorous pitcher plant, Sarracenia purpurea, contain a microscopic aquatic food web that is considered a model system in ecological research. The species identity of the intermediate and top trophic level of this food web, as well the detritivore midge, are highly similar across the native geographic range of S. purpurea and, in some cases, appear to have co-evolved with the plant. However, until recently, the identity, geographic variation, and diversity of the bacteria in the bottom trophic level of this food web have remained largely unknown. This study investigated bacterial community composition inside the leaves of S. purpurea to address: 1) variation in bacterial communities at the beginning of succession at the local scale in different areas of the plant’s native geographic range (southern and mid-regional sites) and 2) the impacts of bacterial consumers and other members of the aquatic food web (i.e., insects) on bacterial community structure. Communities from six leaves (one leaf per plant) from New York and Florida study sites were analyzed using 16S ribosomal RNA gene cloning. Each pitcher within each site had a distinct community; however, there was more overlap in bacterial composition within each site than when communities were compared across sites. In contrast, the identity of protozoans and metazoans in this community were similar in species identity both within a site and between the two sites, but abundances differed. Our results indicate that, at least during the beginning of succession, there is no strong selection for bacterial taxa and that there is no core group of bacteria required by the plant to start the decomposition of trapped insects. Co-evolution between the plant and bacteria appears to not have occurred as it has for other members of this community.
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Affiliation(s)
- Sarah M Gray
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America.
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Prakash O, Shouche Y, Jangid K, Kostka JE. Microbial cultivation and the role of microbial resource centers in the omics era. Appl Microbiol Biotechnol 2012; 97:51-62. [PMID: 23138712 DOI: 10.1007/s00253-012-4533-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/19/2012] [Accepted: 10/20/2012] [Indexed: 11/25/2022]
Abstract
Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, Maharashtra, 411007, India.
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Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A, Watson DB, Brooks SC, Kostka JE. Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 2012; 62:2457-2462. [DOI: 10.1099/ijs.0.035840-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus
Rhodanobacter
shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus
Rhodanobacter
. Although strains 2APBS1T and 116-2 shared high 16S rRNA gene sequence similarity with
Rhodanobacter thiooxydans
LCS2T (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a single novel species of the genus
Rhodanobacter
, for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1T ( = DSM 23569T = JCM 17641T).
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Affiliation(s)
- Om Prakash
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL, USA
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
| | - Puja Jasrotia
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
| | - Will A. Overholt
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
| | - Andy Canion
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
| | - David B. Watson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott C. Brooks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Joel E. Kostka
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL, USA
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Akob DM, Lee SH, Sheth M, Küsel K, Watson DB, Palumbo AV, Kostka JE, Chin KJ. Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments. Front Microbiol 2012; 3:280. [PMID: 22908009 PMCID: PMC3415069 DOI: 10.3389/fmicb.2012.00280] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/18/2012] [Indexed: 11/25/2022] Open
Abstract
Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.
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Kostka JE, Green SJ, Rishishwar L, Prakash O, Katz LS, Mariño-Ramírez L, Jordan IK, Munk C, Ivanova N, Mikhailova N, Watson DB, Brown SD, Palumbo AV, Brooks SC. Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol 2012; 194:4461-2. [PMID: 22843592 PMCID: PMC3416251 DOI: 10.1128/jb.00871-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 06/04/2012] [Indexed: 11/20/2022] Open
Abstract
We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated.
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Affiliation(s)
- Joel E. Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
| | - Stefan J. Green
- DNA Services Facility, Research Resource Center, University of Illinois, Chicago, Illinois, USA
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Om Prakash
- National Centre for Cell Science, Pune, India
| | - Lee S. Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
| | - I. King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
| | - Christine Munk
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - David B. Watson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Anthony V. Palumbo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Scott C. Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Joye SB, Leifer I, MacDonald IR, Chanton JP, Meile CD, Teske AP, Kostka JE, Chistoserdova L, Coffin R, Hollander D, Kastner M, Montoya JP, Rehder G, Solomon E, Treude T, Villareal TA. Comment on "A persistent oxygen anomaly reveals the fate of spilled methane in the deep Gulf of Mexico". Science 2011; 332:1033; author reply 1033. [PMID: 21617058 DOI: 10.1126/science.1203307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Kessler et al. (Reports, 21 January 2011, p. 312) reported that methane released from the 2010 Deepwater Horizon blowout, approximately 40% of the total hydrocarbon discharge, was consumed quantitatively by methanotrophic bacteria in Gulf of Mexico deep waters over a 4-month period. We find the evidence explicitly linking observed oxygen anomalies to methane consumption ambiguous and extension of these observations to hydrate-derived methane climate forcing premature.
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Affiliation(s)
- Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.
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Abstract
Shewanella putrefaciens, a respiratory facultative anaerobe isolated from the Black Sea, can reduce thiosulfate, sulfite, and elemental sulfur to sulfide readily and quantitatively. This widespread and anaerobically versatile microorganism, which is incapable of reducing sulfate, uses oxidized sulfur intermediates as electron acceptors during the respiratory oxidation of organic matter. Because of its widespread distribution and abundance, it may play a significant role in sulfur and trace metal cycling in the Black Sea and in other marine and freshwater anaerobic environments.
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Wu WM, Carley J, Green SJ, Luo J, Kelly SD, Van Nostrand J, Lowe K, Mehlhorn T, Carroll S, Boonchayanant B, Löfller FE, Watson D, Kemner KM, Zhou J, Kitanidis PK, Kostka JE, Jardine PM, Criddle CS. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environ Sci Technol 2010; 44:5104-5111. [PMID: 20527772 DOI: 10.1021/es1000837] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The effects of nitrate on the stability of reduced, immobilized uranium were evaluated in field experiments at a U.S. Department of Energy site in Oak Ridge, TN. Nitrate (2.0 mM) was injected into a reduced region of the subsurface containing high levels of previously immobilized U(IV). The nitrate was reduced to nitrite, ammonium, and nitrogen gas; sulfide levels decreased; and Fe(II) levels increased then deceased. Uranium remobilization occurred concomitant with nitrite formation, suggesting nitrate-dependent, iron-accelerated oxidation of U(IV). Bromide tracer results indicated changes in subsurface flowpaths likely due to gas formation and/or precipitate. Desorption-adsorption of uranium by the iron-rich sediment impacted uranium mobilization and sequestration. After rereduction of the subsurface through ethanol additions, background groundwater containing high levels of nitrate was allowed to enter the reduced test zone. Aqueous uranium concentrations increased then decreased. Clone library analyses of sediment samples revealed the presence of denitrifying bacteria that can oxidize elemental sulfur, H(2)S, Fe(II), and U(IV) (e.g., Thiobacillus spp.), and a decrease in relative abundance of bacteria that can reduce Fe(III) and sulfate. XANES analyses of sediment samples confirmed changes in uranium oxidation state. Addition of ethanol restored reduced conditions and triggered a short-term increase in Fe(II) and aqueous uranium, likely due to reductive dissolution of Fe(III) oxides and release of sorbed U(VI). After two months of intermittent ethanol addition, sulfide levels increased, and aqueous uranium concentrations gradually decreased to <0.1 microM.
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Affiliation(s)
- Wei-Min Wu
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, USA
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Sitte J, Akob DM, Kaufmann C, Finster K, Banerjee D, Burkhardt EM, Kostka JE, Scheinost AC, Büchel G, Küsel K. Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil. Appl Environ Microbiol 2010; 76:3143-52. [PMID: 20363796 PMCID: PMC2869125 DOI: 10.1128/aem.00051-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/23/2010] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the (35)SO(4)(2-) radiotracer method, was restricted to reduced soil horizons with rates of < or =142 +/- 20 nmol cm(-3) day(-1). Concentrations of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that approximately 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [(13)C]acetate- and [(13)C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined < or =100% during anoxic soil incubations. In contrast to results in other studies, soluble uranium increased in carbon-amended treatments, reaching < or =1,407 nM in solution. Our results suggest that (i) ongoing sulfate reduction in contaminated soil resulted in in situ metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems.
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Affiliation(s)
- Jana Sitte
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Denise M. Akob
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Christian Kaufmann
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Kai Finster
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Dipanjan Banerjee
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Eva-Maria Burkhardt
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Joel E. Kostka
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Andreas C. Scheinost
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Georg Büchel
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Kirsten Küsel
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
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Prakash O, Gihring TM, Dalton DD, Chin KJ, Green SJ, Akob DM, Wanger G, Kostka JE. Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. Int J Syst Evol Microbiol 2010; 60:546-553. [DOI: 10.1099/ijs.0.010843-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32T, was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the Geobacteraceae-specific citrate synthase (gltA) mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus Geobacter and shared 92–98 % 16S rRNA gene and 75–81 % rpoB gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Geobacter uraniireducens Rf4T, according to 16S rRNA gene sequence similarity, strain FRC-32T showed a DNA–DNA relatedness value of 21 %. Cells of strain FRC-32T were Gram-negative, non-spore-forming, curved rods, 1.0–1.5 μm long and 0.3–0.5 μm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus Geobacter. The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 °C and pH 6.7–7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the Geobacter group, strain FRC-32T conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32T was metabolically versatile and, unlike its closest relative, G. uraniireducens, was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with fumarate as the electron acceptor. Thus, based on genotypic, phylogenetic and phenotypic differences, strain FRC-32T is considered to represent a novel species of the genus Geobacter, for which the name Geobacter daltonii sp. nov. is proposed. The type strain is FRC-32T (=DSM 22248T=JCM 15807T).
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Affiliation(s)
- Om Prakash
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
| | - Thomas M. Gihring
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
| | - Dava D. Dalton
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
| | - Kuk-Jeong Chin
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Stefan J. Green
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
| | - Denise M. Akob
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
| | - Greg Wanger
- J. Craig Venter Institute, San Diego, CA 92121, USA
| | - Joel E. Kostka
- Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA
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