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Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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Koike K, Honda R, Aoki M, Yamamoto‐Ikemoto R, Syutsubo K, Matsuura N. A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:497-511. [PMID: 37465846 PMCID: PMC10667660 DOI: 10.1111/1758-2229.13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
The method of spiking synthetic internal standard genes (ISGs) to samples for amplicon sequencing, generating sequences and converting absolute gene numbers from read counts has been used only for phylogenetic markers and has not been applied to functional markers. In this study, we developed ISGs, including gene sequences of the 16S rRNA, pmoA, encoding a subunit of particulate methane monooxygenase and amoA, encoding a subunit of ammonia monooxygenase. We added ISGs to the samples, amplified the target genes and performed amplicon sequencing. For the mock community, the copy numbers converted from read counts using ISGs were equivalent to those obtained by the quantitative real-time polymerase chain reaction (4.0 × 104 versus 4.1 × 104 and 3.0 × 103 versus 4.0 × 103 copies μL-DNA-1 for 16S rRNA and pmoA genes, respectively), but we also identified underestimation, possibly due to primer coverage (7.8 × 102 versus 3.7 × 103 μL-DNA-1 for amoA gene). We then applied this method to environmental samples and analysed phylogeny, functional diversity and absolute quantities. One Methylocystis population was most abundant in the sludge samples [16S rRNA gene (3.8 × 109 copies g-1 ) and the pmoA gene (2.3 × 109 copies g-1 )] and were potentially interrelated. This study demonstrates that ISG spiking is useful for evaluating sequencing data processing and quantifying functional markers.
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Affiliation(s)
- Kazuyoshi Koike
- Graduate School of Natural Science and TechnologyKanazawa UniversityKanazawaJapan
| | - Ryo Honda
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
| | - Masataka Aoki
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | | | - Kazuaki Syutsubo
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
- Research Center for Water Environment Technology, School of Engineeringthe University of TokyoTokyoJapan
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
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Chen X, Liu J, Zhu XY, Xue CX, Yao P, Fu L, Yang Z, Sun K, Yu M, Wang X, Zhang XH. Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole. ISME COMMUNICATIONS 2023; 3:117. [PMID: 37964026 PMCID: PMC10645885 DOI: 10.1038/s43705-023-00327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.
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Affiliation(s)
- Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, 573199, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, 266100, China
| | - Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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5
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Kim J, Hwangbo M, Shih CH, Chu KH. Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation. WATER RESEARCH X 2023; 20:100187. [PMID: 37671037 PMCID: PMC10477051 DOI: 10.1016/j.wroa.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 09/07/2023]
Abstract
Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.
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Affiliation(s)
- Jinha Kim
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
- School of Earth, Environmental and Marine Sciences, The University of Texas – Rio Grande Valley, Brownsville, TX, USA
| | - Chih-Hsuan Shih
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
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Wang Y, Liu D, Wei M, Chen J, Li Y, Zhao F, Zhang Z, Ma Y. Genome-wide identification and expression analyses of Toll-like receptors provide new insights on adaptation to intertidal benthic environments in Urechis unicinctus (Annelida, Echiura). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 260:106594. [PMID: 37263159 DOI: 10.1016/j.aquatox.2023.106594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
Toll-like receptors (TLR) are an important class of pattern recognition receptors involved in innate immunity that recognize pathogen-associated and damage-associated molecular patterns. Although the role of TLRs in immunity has been extensively studied, a systematic investigation of their function in environmental adaptation is still in its infancy. In this study, a genome-wide search was conducted to systematically investigate TLR family members of Urechis unicinctus, a typical benthic organism in intertidal mudflats. A total of 28 TLR genes were identified in the U. unicinctus genome, and their fundamental physiological and biochemical properties were characterized. Gene copy number analysis among species in different habitats indicated that TLR family gene expansion may be probably related with benthic environmental adaptation. To further investigate the expression patterns of TLR members under environmental stress, transcriptome data was analyzed from different developmental stages and the hindgut under sulfide stress. Transcriptome analysis of different developmental stages showed that most TLR genes were highly expressed during a key period of benthic environment adaptation (worm-shaped larva). Transcriptome analysis of the hindgut under sulfide stress showed that the expression of 12 TLR members was significantly induced under sulfide stress. These results indicate that the regulation of TLR gene expression may be probably involved in the adaptation of U. unicinctus to the benthic intertidal zone environment. Taken together, this study may lay the foundation for future functional analysis of the specific role of TLRs in host immune responses against sulfide exposure and benthic environmental stress in annelid.
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Affiliation(s)
- Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yunpeng Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Orsi WD. Quantitative microbial ecology: Future challenges and opportunities. Environ Microbiol 2023; 25:91-96. [PMID: 36163700 DOI: 10.1111/1462-2920.16204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 01/21/2023]
Affiliation(s)
- William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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8
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Coskun ÖK, Gomez-Saez GV, Beren M, Ozcan D, Hosgormez H, Einsiedl F, Orsi WD. Carbon metabolism and biogeography of candidate phylum " Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey. Front Microbiol 2023; 14:1063139. [PMID: 36910224 PMCID: PMC9992828 DOI: 10.3389/fmicb.2023.1063139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023] Open
Abstract
Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Dogacan Ozcan
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Hakan Hosgormez
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Florian Einsiedl
- Chair of Hydrogeology, TUM School of Engineering and Design, Technical University of Munich, Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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Perez‐Molphe‐Montoya E, Küsel K, Overholt WA. Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota. Environ Microbiol 2022; 24:5437-5449. [DOI: 10.1111/1462-2920.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kirsten Küsel
- Institute of Biodiversity Friedrich Schiller University Jena Germany
- The German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐ Leipzig Germany
| | - Will A. Overholt
- Institute of Biodiversity Friedrich Schiller University Jena Germany
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10
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Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf. Appl Environ Microbiol 2022; 88:e0021622. [PMID: 35404072 PMCID: PMC9088280 DOI: 10.1128/aem.00216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.
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11
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Orsi WD, Vuillemin A, Coskun ÖK, Rodriguez P, Oertel Y, Niggemann J, Mohrholz V, Gomez-Saez GV. Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis. THE ISME JOURNAL 2022; 16:1245-1261. [PMID: 34893690 PMCID: PMC9038920 DOI: 10.1038/s41396-021-01169-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Fungi are ubiquitous in the ocean and hypothesized to be important members of marine ecosystems, but their roles in the marine carbon cycle are poorly understood. Here, we use 13C DNA stable isotope probing coupled with phylogenetic analyses to investigate carbon assimilation within diverse communities of planktonic and benthic fungi in the Benguela Upwelling System (Namibia). Across the redox stratified water column and in the underlying sediments, assimilation of 13C-labeled carbon from diatom extracellular polymeric substances (13C-dEPS) by fungi correlated with the expression of fungal genes encoding carbohydrate-active enzymes. Phylogenetic analysis of genes from 13C-labeled metagenomes revealed saprotrophic lineages related to the facultative yeast Malassezia were the main fungal foragers of pelagic dEPS. In contrast, fungi living in the underlying sulfidic sediments assimilated more 13C-labeled carbon from chemosynthetic bacteria compared to dEPS. This coincided with a unique seafloor fungal community and dissolved organic matter composition compared to the water column, and a 100-fold increased fungal abundance within the subseafloor sulfide-nitrate transition zone. The subseafloor fungi feeding on 13C-labeled chemolithoautotrophs under anoxic conditions were affiliated with Chytridiomycota and Mucoromycota that encode cellulolytic and proteolytic enzymes, revealing polysaccharide and protein-degrading fungi that can anaerobically decompose chemosynthetic necromass. These subseafloor fungi, therefore, appear to be specialized in organic matter that is produced in the sediments. Our findings reveal that the phylogenetic diversity of fungi across redox stratified marine ecosystems translates into functionally relevant mechanisms helping to structure carbon flow from primary producers in marine microbiomes from the surface ocean to the subseafloor.
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McKay LJ, Smith HJ, Barnhart EP, Schweitzer HD, Malmstrom RR, Goudeau D, Fields MW. Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. THE ISME JOURNAL 2022; 16:915-926. [PMID: 34689183 PMCID: PMC8941128 DOI: 10.1038/s41396-021-01139-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
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Affiliation(s)
- Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Arctic University of Norway, Tromsø, Norway
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6523362. [DOI: 10.1093/femsec/fiac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
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14
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel SE, Eisenreich W, Orsi WD. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME JOURNAL 2021; 16:257-271. [PMID: 34312482 PMCID: PMC8692406 DOI: 10.1038/s41396-021-01066-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frieder Klein
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Susanna E Sichel
- Departamento de Geologia e Geofísica/LAGEMAR-Universidade Federal Fluminense-Brazil, Niterói, RJ, Brazil
| | - Wolfgang Eisenreich
- Department of Chemistry, Bavarian NMR Center-Structural Membrane Biochemistry, Technische Universität München, Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany. .,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
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Suominen S, Dombrowski N, Sinninghe Damsté JS, Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environ Microbiol 2021; 23:2709-2728. [PMID: 31858660 PMCID: PMC8359207 DOI: 10.1111/1462-2920.14902] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/27/2022]
Abstract
Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
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Suominen S, van Vliet DM, Sánchez-Andrea I, van der Meer MTJ, Sinninghe Damsté JS, Villanueva L. Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments. Front Microbiol 2021; 12:628301. [PMID: 34025597 PMCID: PMC8131844 DOI: 10.3389/fmicb.2021.628301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Daan M. van Vliet
- Wageningen Food and Biobased Research (WFBR), Bornse Weilanden 9, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | | | - Marcel T. J. van der Meer
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Recovery and Community Succession of the Zostera marina Rhizobiome after Transplantation. Appl Environ Microbiol 2021; 87:AEM.02326-20. [PMID: 33187993 DOI: 10.1128/aem.02326-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
Seagrasses can form mutualisms with their microbiomes that facilitate the exchange of energy sources, nutrients, and hormones and ultimately impact plant stress resistance. Little is known about community succession within the belowground seagrass microbiome after disturbance and its potential role in the plant's recovery after transplantation. We transplanted Zostera marina shoots with and without an intact rhizosphere and cultivated plants for 4 weeks while characterizing microbiome recovery and effects on plant traits. Rhizosphere and root microbiomes were compositionally distinct, likely representing discrete microbial niches. Furthermore, microbiomes of washed transplants were initially different from those of sod transplants and recovered to resemble an undisturbed state within 14 days. Conspicuously, changes in the microbial communities of washed transplants corresponded with changes in the rhizosphere sediment mass and root biomass, highlighting the strength and responsive nature of the relationship between plants, their microbiome, and the environment. Potential mutualistic microbes that were enriched over time include those that function in the cycling and turnover of sulfur, nitrogen, and plant-derived carbon in the rhizosphere environment. These findings highlight the importance and resilience of the seagrass microbiome after disturbance. Consideration of the microbiome will have meaningful implications for habitat restoration practices.IMPORTANCE Seagrasses are important coastal species that are declining globally, and transplantation can be used to combat these declines. However, the bacterial communities associated with seagrass rhizospheres and roots (the microbiome) are often disturbed or removed completely prior to transplantation. The seagrass microbiome benefits seagrasses through metabolite, nutrient, and phytohormone exchange and contributes to the ecosystem services of seagrass meadows by cycling sulfur, nitrogen, and carbon. This experiment aimed to characterize the importance and resilience of the seagrass belowground microbiome by transplanting Zostera marina with and without intact rhizospheres and tracking microbiome and plant morphological recovery over 4 weeks. We found the seagrass microbiome to be resilient to transplantation disturbance, recovering after 14 days. Additionally, microbiome recovery was linked with seagrass morphology, coinciding with increases in the rhizosphere sediment mass and root biomass. The results of this study can be used to include microbiome responses in informing future restoration work.
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Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments. Appl Environ Microbiol 2020; 86:AEM.00877-20. [PMID: 32709727 DOI: 10.1128/aem.00877-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/17/2020] [Indexed: 11/20/2022] Open
Abstract
Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events.IMPORTANCE Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.
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Girard EB, Kaliwoda M, Schmahl WW, Wörheide G, Orsi WD. Biodegradation of textile waste by marine bacterial communities enhanced by light. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:406-418. [PMID: 32410317 DOI: 10.1111/1758-2229.12856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of biofilm formation on pollutants in the marine realm is expanding, but how communities respond to substrates during colonization remains poorly understood. Here, we assess community assembly and respiration in response to two different micropollutants, virgin high-density polyethylene (HDPE) microbeads and textile fibres under different light settings. Raman characterization, high-throughput DNA sequencing data, quantitative PCR, and respiration measurements reveal how a stimulation of aerobic respiration by micropollutants is translated into selection for significantly different communities colonizing the substrates. Despite the lack of evidence for biodegradation of HDPE, an increased abundance and respiration of bacterial taxa closely related to hydrocarbonoclastic Kordiimonas spp. and Alteromonas spp. in the presence of textile waste highlights their biodegradation potential. Incubations with textile fibres exhibited significantly higher respiration rates in the presence of light, which could be partially explained by photochemical dissolution of the textile waste into smaller bioavailable compounds. Our results suggest that the development and increased respiration of these unique microbial communities may potentially play a role in the bioremediation of the relatively long-lived textile pollutants in marine habitats, and that the respiration of heterotrophic hydrocarbon-degrading bacteria colonizing marine pollutants can be stimulated by light.
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Affiliation(s)
- Elsa B Girard
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Melanie Kaliwoda
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Mineralogische Staatssammlung München, München, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, 80333, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, 80333, Germany
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Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. Methods Mol Biol 2020; 2046:137-149. [PMID: 31407302 DOI: 10.1007/978-1-4939-9721-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.
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Nelson WC, Graham EB, Crump AR, Fansler SJ, Arntzen EV, Kennedy DW, Stegen JC. Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome. PLoS One 2020; 15:e0228165. [PMID: 31986180 PMCID: PMC6984685 DOI: 10.1371/journal.pone.0228165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022] Open
Abstract
Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness—defined as the number of unique within-gene phylotypes—across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.
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Affiliation(s)
- William C. Nelson
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Alex R. Crump
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah J. Fansler
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Evan V. Arntzen
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David W. Kennedy
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - James C. Stegen
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
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Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments. Nat Microbiol 2019; 5:248-255. [PMID: 31873205 DOI: 10.1038/s41564-019-0630-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023]
Abstract
The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation5-7, but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor. Lokiarchaeon gene expression was significantly different across a hypoxic-sulfidic redox gradient, whereby genes involved in growth, fermentation and H2-dependent carbon fixation had the highest expression under the most reducing (sulfidic) conditions. Quantitative stable isotope probing revealed that anaerobic utilization of CO2 and diatomaceous extracellular polymeric substances by Lokiarchaeon was higher than the bacterial average, consistent with higher expression of Lokiarchaeon genes, including those involved in transport and fermentation of sugars and amino acids. The quantitative stable isotope probing and gene expression data demonstrate homoacetogenic activity of Candidatus Lokiarchaeota, whereby fermentative H2 production from organic substrates is coupled with the Wood-Ljungdahl carbon fixation pathway8. The high energetic efficiency provided by homoacetogenesis8 helps to explain the elevated metabolic activity of Lokiarchaeon in this anoxic, energy-limited setting.
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Vuillemin A, Wankel SD, Coskun ÖK, Magritsch T, Vargas S, Estes ER, Spivack AJ, Smith DC, Pockalny R, Murray RW, D’Hondt S, Orsi WD. Archaea dominate oxic subseafloor communities over multimillion-year time scales. SCIENCE ADVANCES 2019; 5:eaaw4108. [PMID: 31223656 PMCID: PMC6584578 DOI: 10.1126/sciadv.aaw4108] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Scott D. Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ömer K. Coskun
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Tobias Magritsch
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Emily R. Estes
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Arthur J. Spivack
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - David C. Smith
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Richard W. Murray
- Department of Earth and Environment, Boston University, Boston, MA 02215, USA
| | - Steven D’Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
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Stal LJ, Bolhuis H, Cretoiu MS. Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities. Environ Microbiol 2018; 21:1529-1551. [PMID: 30507057 DOI: 10.1111/1462-2920.14494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023]
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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Affiliation(s)
- Lucas J Stal
- IBED Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Mariana S Cretoiu
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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Ortega-Arbulú AS, Pichler M, Vuillemin A, Orsi WD. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ Microbiol 2018; 21:374-388. [PMID: 30411473 PMCID: PMC7379666 DOI: 10.1111/1462-2920.14469] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022]
Abstract
Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O2 depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O2 concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.
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Affiliation(s)
- Ana-Sofia Ortega-Arbulú
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Monica Pichler
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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