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Park SY, Zhang Y, O'Loughlin EJ, Jo HY, Kwon JS, Kwon MJ. Temperature-dependent microbial reactions by indigenous microbes in bentonite under Fe(III)- and sulfate-reducing conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133318. [PMID: 38154187 DOI: 10.1016/j.jhazmat.2023.133318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/09/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
Bentonite is a promising buffer material for constructing spent nuclear fuel (SNF) repositories. However, indigenous microbes in bentonite can be introduced to the repository and subsequent sealing of the repository develops anoxic conditions over time which may stimulate fermentation and anaerobic respiration, possibly affecting bentonite structure and SNF repository stability. Moreover, the microbial activity in the bentonite can be impacted by the heat generated from radionuclides decay. Therefore, to investigate the temperature effect on microbial activities in bentonite, we created microcosms with WRK bentonil (a commercial bentonite) using lactate as the electron donor, and sulfate and/or ferrihydrite (Fe(III)) as electron acceptors with incubation at 18 ℃ and 50 ℃. Indigenous WRK microbes reduced sulfate and Fe(III) at both temperatures but with different rates and extents. Lactate was metabolized to acetate at both temperatures, but only to propionate at 18 ℃ during early-stage microbial fermentation. More Fe(III)-reduction at 18 ℃ but more sulfate-reduction at 50 ℃ was observed. Thermophilic and/or metabolically flexible microbes were involved in both fermentation and Fe(III)/sulfate reduction. Our findings illustrate the necessity of considering the influence of temperature on microbial activities when employing bentonite as an engineered buffer material in construction of SNF repository barriers.
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Affiliation(s)
- Su-Young Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | | | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jang-Soon Kwon
- Korea Atomic Energy Research Institute, Daejeon 34057, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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2
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Yin X, Zhou G, Wang H, Han D, Maeke M, Richter-Heitmann T, Wunder LC, Aromokeye DA, Zhu QZ, Nimzyk R, Elvert M, Friedrich MW. Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments. THE ISME JOURNAL 2024; 18:wrad014. [PMID: 38365251 PMCID: PMC10811731 DOI: 10.1093/ismejo/wrad014] [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: 11/10/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/18/2024]
Abstract
Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- School of Resources and Environmental Engineering, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- College of Urban and Environmental Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si 25457, Republic of Korea
| | - Mara Maeke
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Tim Richter-Heitmann
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Lea C Wunder
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Strasse 2-4, Bremen D-28359, Germany
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
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3
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Plum-Jensen LE, Schramm A, Marshall IPG. First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode. Syst Appl Microbiol 2024; 47:126487. [PMID: 38295603 DOI: 10.1016/j.syapm.2024.126487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/23/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024]
Abstract
Cable bacteria are electrically conductive, filamentous Desulfobulbaceae, which are morphologically, functionally, and phylogenetically distinct from the other members of this family. Cable bacteria have not been obtained in pure culture and were therefore previously described as candidate genera, Candidatus Electrothrix and Ca. Electronema; a representative of the latter is available as single-strain sediment enrichment. Here we present an improved workflow to obtain the first single-strain enrichments of Ca. Electrothrix and report their metagenome-assembled genomes (MAGs) and morphology. Based on these results and on previously published high-quality MAGs and morphological data of cable bacteria from both candidate genera, we propose to adopt the genus names Electrothrix and Electronema following the rules of the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), with Electrothrix communis RBTS and Electronema aureum GSTS, respectively, as the nomenclatural types of the genera. Furthermore, based on average nucleotide identity (ANI) values < 95 % with any described species, we propose two of our three single-strain enrichment cultures as novel species of the genus Electrothrix, with the names E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., according to the SeqCode.
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Affiliation(s)
- Lea E Plum-Jensen
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Ian P G Marshall
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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4
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Halevy I, Fike DA, Pasquier V, Bryant RN, Wenk CB, Turchyn AV, Johnston DT, Claypool GE. Sedimentary parameters control the sulfur isotope composition of marine pyrite. Science 2023; 382:946-951. [PMID: 37995229 DOI: 10.1126/science.adh1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Reconstructions of coupled carbon, oxygen, and sulfur cycles rely heavily on sedimentary pyrite sulfur isotope compositions (δ34Spyr). With a model of sediment diagenesis, paired with global datasets of sedimentary parameters, we show that the wide range of δ34Spyr (~100 per mil) in modern marine sediments arises from geographic patterns in the relative rates of diffusion, burial, and microbial reduction of sulfate. By contrast, the microbial sulfur isotope fractionation remains large and relatively uniform. Over Earth history, the effect of increasing seawater sulfate and oxygen concentrations on sulfate and sulfide transport and reaction may explain the corresponding increase observed in the δ34S offset between sulfate and pyrite. More subtle variations may be related to changes in depositional environments associated with sea level fluctuations and supercontinent cycles.
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Affiliation(s)
- I Halevy
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - D A Fike
- Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130-4899, USA
| | - V Pasquier
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - R N Bryant
- Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130-4899, USA
- Earth, Atmospheric and Planetary Sciences, Purdue University, W. Lafayette, IN 47907, USA
| | - C B Wenk
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - A V Turchyn
- Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
| | - D T Johnston
- Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - G E Claypool
- 8910 West Jewell Avenue, Unit 209, Lakewood, CO 80232, USA
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5
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Sun CS, Zhou LY, Liang QY, Wang XM, Lei YX, Xu ZX, Wang FQ, Chen GJ, Du ZJ, Mu DS. Short-chain fatty acids (SCFAs) as potential resuscitation factors that promote the isolation and culture of uncultured bacteria in marine sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:400-414. [PMID: 37637259 PMCID: PMC10449756 DOI: 10.1007/s42995-023-00187-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/20/2023] [Indexed: 08/29/2023]
Abstract
Many marine bacteria are difficult to culture because they are dormant, rare or found in low-abundances. Enrichment culturing has been widely tested as an important strategy to isolate rare or dormant microbes. However, many more mechanisms remain uncertain. Here, based on 16S rRNA gene high-throughput sequencing and metabolomics technology, it was found that the short-chain fatty acids (SCFAs) in metabolites were significantly correlated with uncultured bacterial groups during enrichment cultures. A pure culture analysis showed that the addition of SCFAs to media also resulted in high efficiency for the isolation of uncultured strains from marine sediments. As a result, 238 strains belonging to 10 phyla, 26 families and 82 species were successfully isolated. Some uncultured rare taxa within Chlorobi and Kiritimatiellaeota were successfully cultured. Amongst the newly isolated uncultured microbes, most genomes, e.g. bacteria, possess SCFA oxidative degradation genes, and these features might aid these microbes in better adapting to the culture media. A further resuscitation analysis of a viable but non-culturable (VBNC) Marinilabiliales strain verified that the addition of SCFAs could break the dormancy of Marinilabiliales in 5 days, and the growth curve test showed that the SCFAs could shorten the lag phase and increase the growth rate. Overall, this study provides new insights into SCFAs, which were first studied as resuscitation factors in uncultured marine bacteria. Thus, this study can help improve the utilisation and excavation of marine microbial resources, especially for the most-wanted or key players. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00187-w.
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Affiliation(s)
- Chun-Shui Sun
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
| | - Liu-Yan Zhou
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000 China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209 China
| | - Xiao-Man Wang
- Tancheng County Inspection and Testing Center, Tancheng, 276100 China
| | - Yi-Xuan Lei
- Marine College, Shandong University, Weihai, 264209 China
| | - Zhen-Xing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657 Japan
| | - Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209 China
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6
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Jaussi M, Jørgensen BB, Kjeldsen KU, Lomstein BA, Pearce C, Seidenkantz MS, Røy H. Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere. Front Microbiol 2023; 14:1198664. [PMID: 37555068 PMCID: PMC10405931 DOI: 10.3389/fmicb.2023.1198664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.
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Affiliation(s)
- Marion Jaussi
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | | | | | - Christof Pearce
- Department of Geoscience, Aarhus University, Aarhus, Denmark
| | | | - Hans Røy
- Department of Biology, Aarhus University, Aarhus, Denmark
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7
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Ngere J, Ebrahimi KH, Williams R, Pires E, Walsby-Tickle J, McCullagh JSO. Ion-Exchange Chromatography Coupled to Mass Spectrometry in Life Science, Environmental, and Medical Research. Anal Chem 2023; 95:152-166. [PMID: 36625129 PMCID: PMC9835059 DOI: 10.1021/acs.analchem.2c04298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Judith
B. Ngere
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kourosh H. Ebrahimi
- Institute
of Pharmaceutical Science, King’s
College London, London SE1 9NH, U.K.
| | - Rachel Williams
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Elisabete Pires
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - John Walsby-Tickle
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James S. O. McCullagh
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,
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8
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Mechanism of Electron Acceptor Promoting Propionic Acid Transformation in Anaerobic Fermentation. ENERGIES 2022. [DOI: 10.3390/en15113947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To improve the conversion efficiency of propionic acid in the post-anaerobic fermentation of biogas slurry, the anaerobic fermentation process using biogas slurry with a high acid content was simulated in an anaerobic reactor at 35 ± 0.5 °C using sodium propionate as the sole substrate. The effects of different electron acceptors (NO3−, SO42− and Fe3+) on propionic acid conversion and the succession of microbial community structures were investigated. The results showed that the experimental group with the electron acceptor NO3− exhibited the best anaerobic fermentation effect, with a maximum propionate removal rate of 94%, which was 36% higher than the control group without an electron acceptor. The maximum methane production rate was 307.6 mL/g COD, an increase of 30% compared with the control group. Thauera, Aquabacterium, Desulfomicrobium, Clostridium_sensu_stricto_1, and other functional microorganisms were all enriched. The dominant functional genes related to redox reactions, such as K03711, K00384, and K03406, were highly enriched in the reactor when Fe3+ and NO3− were added. The study shows that adding an electron acceptor can enhance interactions between microorganisms, achieve efficient propionate conversion, and improve methane production in the system.
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9
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Phylogenetic diversity in sulphate-reducing bacterial communities from oxidised and reduced bottom sediments of the Barents Sea. Antonie van Leeuwenhoek 2022; 115:801-820. [DOI: 10.1007/s10482-022-01733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 11/25/2022]
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10
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Voskuhl L, Brusilova D, Brauer VS, Meckenstock RU. Inhibition of sulfate-reducing bacteria with formate. FEMS Microbiol Ecol 2022; 98:6510814. [PMID: 35040992 PMCID: PMC8831227 DOI: 10.1093/femsec/fiac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8 or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Concerning D. multivorans, increasing formate concentrations delayed the onsets of growth and sulfate reduction, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
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Affiliation(s)
- L Voskuhl
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - D Brusilova
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - V S Brauer
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - R U Meckenstock
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
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11
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Response to substrate limitation by a marine sulfate-reducing bacterium. THE ISME JOURNAL 2022; 16:200-210. [PMID: 34285365 PMCID: PMC8692349 DOI: 10.1038/s41396-021-01061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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12
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Pelikan C, Wasmund K, Glombitza C, Hausmann B, Herbold CW, Flieder M, Loy A. Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment. THE ISME JOURNAL 2021; 15:833-847. [PMID: 33208892 PMCID: PMC8027456 DOI: 10.1038/s41396-020-00817-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 01/30/2023]
Abstract
Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.
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Affiliation(s)
- Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Austrian Polar Research Institute, Vienna, Austria.
| | - Clemens Glombitza
- Department of Biology, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Bela Hausmann
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Mathias Flieder
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Austrian Polar Research Institute, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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13
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Physicochemical and biological controls of sulfide accumulation in a high temperature oil reservoir. Appl Microbiol Biotechnol 2020; 104:8467-8478. [DOI: 10.1007/s00253-020-10828-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/02/2020] [Accepted: 08/11/2020] [Indexed: 01/04/2023]
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14
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Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments. ISME JOURNAL 2020; 14:1345-1358. [PMID: 32066876 DOI: 10.1038/s41396-020-0615-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/30/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities, and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR margin and compare them to their relatives from shallower settings. We describe 31 MAGs of six different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales, and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capability of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite, and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducing bacteria. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl coenzyme M reductase complex and encodes a noncanonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljungdahl pathway. These metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work expands our knowledge about the metabolic functional repertoire of marine benthic archaea.
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15
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Jørgensen BB, Andrén T, Marshall IPG. Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea. Environ Microbiol 2020; 22:1688-1706. [PMID: 31970880 DOI: 10.1111/1462-2920.14920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
Abstract
The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.
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Affiliation(s)
- Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Thomas Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Center for Electromicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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16
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Pelikan C, Jaussi M, Wasmund K, Seidenkrantz MS, Pearce C, Kuzyk ZZA, Herbold CW, Røy H, Kjeldsen KU, Loy A. Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments. Front Microbiol 2019; 10:2558. [PMID: 31787951 PMCID: PMC6853847 DOI: 10.3389/fmicb.2019.02558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.
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Affiliation(s)
- Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marion Jaussi
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marit-Solveig Seidenkrantz
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Christof Pearce
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Zou Zou Anna Kuzyk
- Department of Geological Sciences, Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB, Canada
| | - Craig W. Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Hans Røy
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
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17
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Eickenbusch P, Takai K, Sissman O, Suzuki S, Menzies C, Sakai S, Sansjofre P, Tasumi E, Bernasconi SM, Glombitza C, Jørgensen BB, Morono Y, Lever MA. Origin of Short-Chain Organic Acids in Serpentinite Mud Volcanoes of the Mariana Convergent Margin. Front Microbiol 2019; 10:1729. [PMID: 31404165 PMCID: PMC6677109 DOI: 10.3389/fmicb.2019.01729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/12/2019] [Indexed: 11/17/2022] Open
Abstract
Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H2), methane (CH4), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H2 concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H2, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H2 data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δ13C-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.
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Affiliation(s)
- Philip Eickenbusch
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Ken Takai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Shino Suzuki
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Catriona Menzies
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, United Kingdom.,Department of Geology and Petroleum Geology, University of Aberdeen, Aberdeen, United Kingdom
| | - Sanae Sakai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | - Pierre Sansjofre
- Laboratoire Géosciences Océan UMR 6538, Université de Bretagne Occidentale, Brest, France
| | - Eiji Tasumi
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Clemens Glombitza
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Yuki Morono
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
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18
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Dissimilatory reduction of Fe(III) by a novel Serratia marcescens strain with special insight into the influence of prodigiosin. Int Microbiol 2019; 23:201-214. [DOI: 10.1007/s10123-019-00088-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022]
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19
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019; 10:849. [PMID: 31105660 PMCID: PMC6492693 DOI: 10.3389/fmicb.2019.00849] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.
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Affiliation(s)
- Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
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21
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Schwab VF, Nowak ME, Elder CD, Trumbore SE, Xu X, Gleixner G, Lehmann R, Pohnert G, Muhr J, Küsel K, Totsche KU. 14C-Free Carbon Is a Major Contributor to Cellular Biomass in Geochemically Distinct Groundwater of Shallow Sedimentary Bedrock Aquifers. WATER RESOURCES RESEARCH 2019; 55:2104-2121. [PMID: 31068736 PMCID: PMC6487957 DOI: 10.1029/2017wr022067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 09/17/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Despite the global significance of the subsurface biosphere, the degree to which it depends on surface organic carbon (OC) is still poorly understood. Here, we compare stable and radiogenic carbon isotope compositions of microbial phospholipid fatty acids (PLFAs) with those of in situ potential microbial C sources to assess the major C sources for subsurface microorganisms in biogeochemical distinct shallow aquifers (Critical Zone Exploratory, Thuringia Germany). Despite the presence of younger OC, the microbes assimilated 14C-free OC to varying degrees; ~31% in groundwater within the oxic zone, ~47% in an iron reduction zone, and ~70% in a sulfate reduction/anammox zone. The persistence of trace amounts of mature and partially biodegraded hydrocarbons suggested that autochthonous petroleum-derived hydrocarbons were a potential 14C-free C source for heterotrophs in the oxic zone. In this zone, Δ14C values of dissolved inorganic carbon (-366 ± 18‰) and 11MeC16:0 (-283 ± 32‰), an important component in autotrophic nitrite oxidizers, were similar enough to indicate that autotrophy is an important additional C fixation pathway. In anoxic zones, methane as an important C source was unlikely since the 13C-fractionations between the PLFAs and CH4 were inconsistent with kinetic isotope effects associated with methanotrophy. In the sulfate reduction/anammox zone, the strong 14C-depletion of 10MeC16:0 (-942 ± 22‰), a PLFA common in sulfate reducers, indicated that those bacteria were likely to play a critical part in 14C-free sedimentary OC cycling. Results indicated that the 14C-content of microbial biomass in shallow sedimentary aquifers results from complex interactions between abundance and bioavailability of naturally occurring OC, hydrogeology, and specific microbial metabolisms.
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Affiliation(s)
- Valérie F. Schwab
- Institute of GeosciencesFriedrich Schiller UniversityJenaGermany
- Max‐Planck‐Institute for BiogeochemistryJenaGermany
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller UniversityJenaGermany
| | | | - Clayton D. Elder
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - Susan E. Trumbore
- Max‐Planck‐Institute for BiogeochemistryJenaGermany
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - Xiaomei Xu
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | | | - Robert Lehmann
- Institute of GeosciencesFriedrich Schiller UniversityJenaGermany
| | - Georg Pohnert
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller UniversityJenaGermany
| | - Jan Muhr
- Max‐Planck‐Institute for BiogeochemistryJenaGermany
| | - Kirsten Küsel
- Institute of EcologyFriedrich Schiller UniversityJenaGermany
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigGermany
| | - Kai U. Totsche
- Institute of GeosciencesFriedrich Schiller UniversityJenaGermany
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22
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Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. Appl Environ Microbiol 2019; 85:AEM.02164-18. [PMID: 30504213 PMCID: PMC6365825 DOI: 10.1128/aem.02164-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/17/2018] [Indexed: 11/23/2022] Open
Abstract
Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments. Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities. IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.
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23
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Montag D, Schink B. Formate and Hydrogen as Electron Shuttles in Terminal Fermentations in an Oligotrophic Freshwater Lake Sediment. Appl Environ Microbiol 2018; 84:e01572-18. [PMID: 30097443 PMCID: PMC6182907 DOI: 10.1128/aem.01572-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/03/2018] [Indexed: 11/20/2022] Open
Abstract
The energetic situation of terminal fermentations in methanogenesis was analyzed by pool size determinations in sediment cores taken in the oligotrophic Lake Constance, Germany. Distribution profiles of fermentation intermediates and products were measured at three different water depths (2, 10, and 80 m). Methane concentrations were constant below 10 cm of sediment depth. Within the methanogenic zone, concentrations of formate, acetate, propionate, and butyrate varied between 1 and 40 μM, and hydrogen was between 0.5 and 5 Pa. From the distribution profiles of the fermentation intermediates, Gibbs free energy changes for their interconversion were calculated. Pool sizes of formate and hydrogen were energetically nearly equivalent, with -5 ± 5 kJ per mol difference of free energy change (ΔG) for a hypothetical conversion of formate to hydrogen plus CO2 The ΔG values for conversion of fatty acids to methanogenic substrates and their further conversion to methane and CO2 were calculated with hydrogen and with formate as intermediates. Syntrophic propionate oxidation reached energetic equilibrium with formate as the sole electron carrier but was sufficiently exergonic if at least some of the electrons were transferred via hydrogen. The energetic consequences of formate versus hydrogen transfer in secondary and methanogenic fermentations indicate that both carrier systems are probably used simultaneously to optimize the energy yields for the partners involved.IMPORTANCE In the terminal steps of methane formation in freshwater lake sediments, fermenting bacteria cooperate syntrophically with methanogens and homoacetogens at minimum energy increments via interspecies electron transfer. The energy yields of the partner organisms in these cooperations have so far been calculated based mainly on in situ hydrogen partial pressures. In the present study, we also analyzed pools of formate as an alternative electron carrier in sediment cores of an oligotrophic lake. The formate and hydrogen pools appeared to be energetically nearly equivalent and are likely to be used simultaneously for interspecies electron transfer. Calculations of reaction energies of the partners involved suggest that propionate degradation may also proceed through the Smithella pathway, which converts propionate via butyrate and acetate to three acetate residues, thus circumventing one energetically difficult fatty acid oxidation step.
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Affiliation(s)
- Dominik Montag
- Department of Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany
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24
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Cryptic CH 4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea. ISME JOURNAL 2018; 13:250-262. [PMID: 30194429 DOI: 10.1038/s41396-018-0273-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/10/2018] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.
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25
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Müller AL, Pelikan C, de Rezende JR, Wasmund K, Putz M, Glombitza C, Kjeldsen KU, Jørgensen BB, Loy A. Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment. Environ Microbiol 2018; 20:2927-2940. [PMID: 30051650 PMCID: PMC6175234 DOI: 10.1111/1462-2920.14297] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/02/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022]
Abstract
Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Albert L. Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Julia R. de Rezende
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Martina Putz
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | | | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
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Møller MH, Glombitza C, Lever MA, Deng L, Morono Y, Inagaki F, Doll M, Su CC, Lomstein BA. D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin. Front Microbiol 2018; 9:967. [PMID: 29867871 PMCID: PMC5963217 DOI: 10.3389/fmicb.2018.00967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 108 to 106 cells cm-3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 108 cells cm-3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %TAAC (percentage of total organic carbon present as amino acid carbon), %TAAN (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.
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Affiliation(s)
- Mikkel H Møller
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Clemens Glombitza
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,National Aeronautics and Space Administration-Ames Research Center, Moffett Field, CA, United States
| | - Mark A Lever
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Longhui Deng
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Mechthild Doll
- Faculty of Geosciences (FB 05), University of Bremen, Bremen, Germany
| | - Chin-Chia Su
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
| | - Bente A Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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27
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Antler G, Pellerin A. A Critical Look at the Combined Use of Sulfur and Oxygen Isotopes to Study Microbial Metabolisms in Methane-Rich Environments. Front Microbiol 2018; 9:519. [PMID: 29681890 PMCID: PMC5898156 DOI: 10.3389/fmicb.2018.00519] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Separating the contributions of anaerobic oxidation of methane and organoclastic sulfate reduction in the overall sedimentary sulfur cycle of marine sediments has benefited from advances in isotope biogeochemistry. Particularly, the coupling of sulfur and oxygen isotopes measured in the residual sulfate pool (δ18OSO4 vs. δ34SSO4). Yet, some important questions remain. Recent works have observed patterns that are inconsistent with previous interpretations. We differentiate the contributions of oxygen and sulfur isotopes to separating the anaerobic oxidation of methane and organoclastic sulfate reduction into three phases; first evidence from conventional high methane vs. low methane sites suggests a clear relationship between oxygen and sulfur isotopes in porewater and the metabolic process taking place. Second, evidence from pure cultures and organic matter rich sites with low levels of methane suggest the signatures of both processes overlap and cannot be differentiated. Third, we take a critical look at the use of oxygen and sulfur isotopes to differentiate metabolic processes (anaerobic oxidation of methane vs. organoclastic sulfate reduction). We identify that it is essential to develop a better understanding of the oxygen kinetic isotope effect, the degree of isotope exchange with sulfur intermediates as well as establishing their relationships with the cell-specific metabolic rates if we are to develop this proxy into a reliable tool to study the sulfur cycle in marine sediments and the geological record.
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Affiliation(s)
- Gilad Antler
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.,The Interuniversity Institute for Marine Sciences, Eilat, Israel
| | - André Pellerin
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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28
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Marshall IP, Karst SM, Nielsen PH, Jørgensen BB. Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition. Mar Genomics 2018; 37:58-68. [DOI: 10.1016/j.margen.2017.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 02/04/2023]
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29
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Control on rate and pathway of anaerobic organic carbon degradation in the seabed. Proc Natl Acad Sci U S A 2017; 115:367-372. [PMID: 29279408 DOI: 10.1073/pnas.1715789115] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The degradation of organic matter in the anoxic seabed proceeds through a complex microbial network in which the terminal steps are dominated by oxidation with sulfate or conversion into methane and CO2 The controls on pathway and rate of the degradation process in different geochemical zones remain elusive. Radiotracer techniques were used to perform measurements of sulfate reduction, methanogenesis, and acetate oxidation with unprecedented sensitivity throughout Holocene sediment columns from the Baltic Sea. We found that degradation rates transition continuously from the sulfate to the methane zone, thereby demonstrating that terminal steps do not exert feedback control on upstream hydrolytic and fermentative processes, as previously suspected. Acetate was a key intermediate for carbon mineralization in both zones. However, acetate was not directly converted into methane. Instead, an additional subterminal step converted acetate to CO2 and reducing equivalents, such as H2, which then fed autotrophic reduction of CO2 to methane.
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30
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Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
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31
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Microbial turnover times in the deep seabed studied by amino acid racemization modelling. Sci Rep 2017; 7:5680. [PMID: 28720809 PMCID: PMC5516024 DOI: 10.1038/s41598-017-05972-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/06/2017] [Indexed: 01/20/2023] Open
Abstract
The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D:L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D:L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments. We applied for the first time newly established constraints on several important input parameters of the D:L-amino acid model, such as a higher aspartic acid racemization rate constant and a lower cell-specific carbon content of sub-seafloor microorganisms. Our model results show that the pool of necromass amino acids is turned over by microbial activity every few thousand years, while the turnover times of vegetative cells are in the order of years to decades. Notably, microbial turnover times in million-year-old sediment from the Peru Margin are up to 100-fold shorter than previous estimates, highlighting the influence of microbial activities on element cycling over geologic time scales.
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32
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Glombitza C, Adhikari RR, Riedinger N, Gilhooly WP, Hinrichs KU, Inagaki F. Microbial Sulfate Reduction Potential in Coal-Bearing Sediments Down to ~2.5 km below the Seafloor off Shimokita Peninsula, Japan. Front Microbiol 2016; 7:1576. [PMID: 27761134 PMCID: PMC5051215 DOI: 10.3389/fmicb.2016.01576] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Sulfate reduction is the predominant anaerobic microbial process of organic matter mineralization in marine sediments, with recent studies revealing that sulfate reduction not only occurs in sulfate-rich sediments, but even extends to deeper, methanogenic sediments at very low background concentrations of sulfate. Using samples retrieved off the Shimokita Peninsula, Japan, during the Integrated Ocean Drilling Program (IODP) Expedition 337, we measured potential sulfate reduction rates by slurry incubations with 35S-labeled sulfate in deep methanogenic sediments between 1276.75 and 2456.75 meters below the seafloor. Potential sulfate reduction rates were generally extremely low (mostly below 0.1 pmol cm-3 d-1) but showed elevated values (up to 1.8 pmol cm-3 d-1) in a coal-bearing interval (Unit III). A measured increase in hydrogenase activity in the coal-bearing horizons coincided with this local increase in potential sulfate reduction rates. This paired enzymatic response suggests that hydrogen is a potentially important electron donor for sulfate reduction in the deep coalbed biosphere. By contrast, no stimulation of sulfate reduction rates was observed in treatments where methane was added as an electron donor. In the deep coalbeds, small amounts of sulfate might be provided by a cryptic sulfur cycle. The isotopically very heavy pyrites (δ34S = +43‰) found in this horizon is consistent with its formation via microbial sulfate reduction that has been continuously utilizing a small, increasingly 34S-enriched sulfate reservoir over geologic time scales. Although our results do not represent in-situ activity, and the sulfate reducers might only have persisted in a dormant, spore-like state, our findings show that organisms capable of sulfate reduction have survived in deep methanogenic sediments over more than 20 Ma. This highlights the ability of sulfate-reducers to persist over geological timespans even in sulfate-depleted environments. Our study moreover represents the deepest evidence of a potential for sulfate reduction in marine sediments to date.
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Affiliation(s)
- Clemens Glombitza
- Department of Biosciences, Center for Geomicrobiology, Aarhus University Aarhus, Denmark
| | - Rishi R Adhikari
- MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Natascha Riedinger
- Boone Pickens School of Geology, Oklahoma State University Stillwater, OK, USA
| | - William P Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis Indianapolis, IN, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and TechnologyKochi, Japan; Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and TechnologyYokohama, Japan; Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
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33
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Braun S, Morono Y, Littmann S, Kuypers M, Aslan H, Dong M, Jørgensen BB, Lomstein BA. Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea. Front Microbiol 2016; 7:1375. [PMID: 27630628 PMCID: PMC5005352 DOI: 10.3389/fmicb.2016.01375] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass.
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Affiliation(s)
- Stefan Braun
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology Kochi, Japan
| | - Sten Littmann
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Marcel Kuypers
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Hüsnü Aslan
- Interdisciplinary Nanoscience Center, Aarhus University Aarhus, Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center, Aarhus University Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Bente Aa Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark; Section for Microbiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
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34
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Laufer K, Byrne JM, Glombitza C, Schmidt C, Jørgensen BB, Kappler A. Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content. Environ Microbiol 2016; 18:3159-74. [DOI: 10.1111/1462-2920.13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/18/2016] [Accepted: 05/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Katja Laufer
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - James M. Byrne
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - Clemens Glombitza
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
| | - Bo Barker Jørgensen
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences; University of Tuebingen; Tuebingen Germany
- Department of Bioscience; Center for Geomicrobiology, Aarhus University; Aarhus Denmark
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35
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Pelikan C, Herbold CW, Hausmann B, Müller AL, Pester M, Loy A. Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics. Environ Microbiol 2016; 18:2994-3009. [PMID: 26625892 DOI: 10.1111/1462-2920.13139] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/18/2015] [Indexed: 01/03/2023]
Abstract
Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.
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Affiliation(s)
- Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Albert L Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria. .,Austrian Polar Research Institute, Vienna, Austria.
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