1
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Onishi Y, Yamanaka T, Koba K. Major contribution of sulfide-derived sulfur to the benthic food web in a large freshwater lake. GEOBIOLOGY 2023; 21:671-685. [PMID: 37434444 DOI: 10.1111/gbi.12569] [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: 01/22/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
In freshwater systems, contributions of chemosynthetic products by sulfur-oxidizing bacteria in sediments as nutritional resources in benthic food webs remain unclear, even though chemosynthetic products might be an important nutritional resource for benthic food webs in deep-sea hydrothermal vents and shallow marine systems. To study geochemical aspects of this trophic pathway, we sampled sediment cores and benthic animals at two sites (90 and 50 m water depths) in the largest freshwater (mesotrophic) lake in Japan: Lake Biwa. Stable carbon, nitrogen, and sulfur isotopes of the sediments and animals were measured to elucidate the sulfur nutritional resources for the benthic food web precisely by calculating the contributions of the incorporation of sulfide-derived sulfur to the biomass and of the biogeochemical sulfur cycle supporting the sulfur nutritional resource. The recovered sediment cores showed increases in 34 S-depleted sulfide at 5 cm sediment depth and showed low sulfide concentration with high δ34 S in deeper layers, suggesting an association of microbial activities with sulfate reduction and sulfide oxidation in the sediments. The sulfur-oxidizing bacteria may contribute to benthic animal biomass. Calculations based on the biomass, sulfur content, and contribution to sulfide-derived sulfur of each animal comprising the benthic food web revealed that 58%-67% of the total biomass sulfur in the benthic food web of Lake Biwa is occupied by sulfide-derived sulfur. Such a large contribution implies that the chemosynthetic products of sulfur-oxidizing bacteria are important nutritional resources supporting benthic food webs in the lake ecosystems, at least in terms of sulfur. The results present a new trophic pathway for sulfur that has been overlooked in lake ecosystems with low-sulfate concentrations.
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Affiliation(s)
- Yuji Onishi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Toshiro Yamanaka
- School of Marine Resources and Environment, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
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2
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Li S, Harir M, Schmitt-Kopplin P, Machado-Silva F, Gonsior M, Bastviken D, Enrich-Prast A, Valle J, Hertkorn N. Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters. ACS ES&T WATER 2023; 3:2083-2095. [PMID: 37588807 PMCID: PMC10425957 DOI: 10.1021/acsestwater.2c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 08/18/2023]
Abstract
Positive and negative electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and 1H NMR revealed major compositional and structural changes of dissolved organic matter (DOM) after mixing two sets of river waters in Amazon confluences: the Solimões and Negro Rivers (S + N) and the Amazon and Tapajós Rivers (A + T). We also studied the effects of water mixing ratios and incubation time on the composition and structure of DOM molecules. NMR spectra demonstrated large-scale structural transformations in the case of S + N mixing, with gain of pure and functionalized aliphatic units and loss of all other structures after 1d incubation. A + T mixing resulted in comparatively minor structural alterations, with a major gain of small aliphatic biomolecular binding motifs. Remarkably, structural alterations from mixing to 1d incubation were in essence reversed from 1d to 5d incubation for both S + N and A + T mixing experiments. Heterotrophic bacterial production (HBP) in endmembers S, N, and S + N mixtures remained near 0.03 μgC L-1 h-1, whereas HBP in A, T, and A + T were about five times higher. High rates of dark carbon fixation took place at S + N mixing in particular. In-depth biogeochemical characterization revealed major distinctions between DOM biogeochemical changes and temporal evolution at these key confluence sites within the Amazon basin.
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Affiliation(s)
- Siyu Li
- Research
Unit Analytical Biogeochemistry, Helmholtz
Munich, Ingolstaedter
Landstrasse 1, Neuherberg 85764, Germany
| | - Mourad Harir
- Research
Unit Analytical Biogeochemistry, Helmholtz
Munich, Ingolstaedter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Food Chemistry, Technische
Universität München, Alte Akademie 10, Freising-Weihenstephan 85354, Germany
| | - Philippe Schmitt-Kopplin
- Research
Unit Analytical Biogeochemistry, Helmholtz
Munich, Ingolstaedter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Food Chemistry, Technische
Universität München, Alte Akademie 10, Freising-Weihenstephan 85354, Germany
| | - Fausto Machado-Silva
- Program
in Geosciences—Environmental Geochemistry, Chemistry Institute, Fluminense Federal University, Niteroi 24020-141, Brazil
- Department
of Environmental Sciences, University of
Toledo, Toledo, Ohio 43606, United States
| | - Michael Gonsior
- Chesapeake
Biological Laboratory, University of Maryland
Center for Environmental Science, Solomons, Maryland 20688, United States
| | - David Bastviken
- Department
of Thematic Studies—Environmental Change, Linköping University, Linköping SE-581 83, Sweden
| | - Alex Enrich-Prast
- Department
of Thematic Studies—Environmental Change and Biogas Solutions
Research Center (BSRC), Linköping
University, Linköping SE-581 83, Sweden
- Multiuser
Unit of Environmental Analysis, University
Federal of Rio de Janeiro, Rio
de Janeiro 11070-100, Brazil
| | - Juliana Valle
- Research
Unit Analytical Biogeochemistry, Helmholtz
Munich, Ingolstaedter
Landstrasse 1, Neuherberg 85764, Germany
| | - Norbert Hertkorn
- Research
Unit Analytical Biogeochemistry, Helmholtz
Munich, Ingolstaedter
Landstrasse 1, Neuherberg 85764, Germany
- Department
of Thematic Studies—Environmental Change and Biogas Solutions
Research Center (BSRC), Linköping
University, Linköping SE-581 83, Sweden
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3
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Li S, Harir M, Schmitt-Kopplin P, Gonsior M, Enrich-Prast A, Bastviken D, Valle J, Machado-Silva F, Hertkorn N. Comprehensive assessment of dissolved organic matter processing in the Amazon River and its major tributaries revealed by positive and negative electrospray mass spectrometry and NMR spectroscopy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159620. [PMID: 36280052 DOI: 10.1016/j.scitotenv.2022.159620] [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: 07/19/2022] [Revised: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Rivers are natural biogeochemical systems shaping the fates of dissolved organic matter (DOM) from leaving soils to reaching the oceans. This study focuses on Amazon basin DOM processing employing negative and positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI[±] FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR) to reveal effects of major processes on the compositional space and structural characteristics of black, white and clear water systems. These include non-conservative mixing at the confluences of (1) Solimões and the Negro River, (2) the Amazon River and the Madeira River, and (3) in-stream processing of Amazon River DOM between the Madeira River and the Tapajós River. The Negro River (black water) supplies more highly oxygenated and high molecular weight compounds, whereas the Solimões and Madeira Rivers (white water) contribute more CHNO and CHOS molecules to the Amazon River main stem. Aliphatic CHO and abundant CHNO compounds prevail in Tapajos River DOM (clear water), likely originating from primary production. Sorption onto particles and heterotrophic microbial degradation are probably the principal mechanisms for the observed changes in DOM composition in the Amazon River and its tributaries.
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Affiliation(s)
- Siyu Li
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität Muenchen, Alte Akademie 10, 85354 Freising-Weihenstephan, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität Muenchen, Alte Akademie 10, 85354 Freising-Weihenstephan, Germany
| | - Michael Gonsior
- University of Maryland Center for Environmental Science, Chesapeake Biological Laboratory, 146 Williams Street, Solomons, MD 20688, United States
| | - Alex Enrich-Prast
- Department of Thematic Studies - Environmental Change, Linköping University, SE-581 83 Linköping, Sweden; Institute of Marine Science, Federal University of São Paolo, Santos, Brazil
| | - David Bastviken
- Department of Thematic Studies - Environmental Change, Linköping University, SE-581 83 Linköping, Sweden
| | - Juliana Valle
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Fausto Machado-Silva
- Program in Geosciences - Environmental Geochemistry, Chemistry Institute, Fluminense Federal University, 24020-141 Niteroi, Brazil; Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.
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Braga LPP, Orland C, Emilson EJS, Fitch AA, Osterholz H, Dittmar T, Basiliko N, Mykytczuk NCS, Tanentzap AJ. Viruses direct carbon cycling in lake sediments under global change. Proc Natl Acad Sci U S A 2022; 119:e2202261119. [PMID: 36206369 PMCID: PMC9564219 DOI: 10.1073/pnas.2202261119] [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: 02/08/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.
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Affiliation(s)
- Lucas P. P. Braga
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
- Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Chloé Orland
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Erik J. S. Emilson
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Amelia A. Fitch
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment and Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, 26129 Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment and Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, 26129 Oldenburg, Germany
| | - Nathan Basiliko
- Vale Living with Lakes Centre, Laurentian University, Sudbury, ON P3E2C6, Canada
| | | | - Andrew J. Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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5
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Liu B, Hou L, Zheng Y, Zhang Z, Tang X, Mao T, Du J, Bi Q, Dong H, Yin G, Han P, Liang X, Liu M. Dark carbon fixation in intertidal sediments: Controlling factors and driving microorganisms. WATER RESEARCH 2022; 216:118381. [PMID: 35381430 DOI: 10.1016/j.watres.2022.118381] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y-1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using 14C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m-2 day-1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM-harboring bacteria, rather than cbbL-harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM-harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus, and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Tieqiang Mao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Qianqian Bi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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6
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Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies. Extremophiles 2021; 26:3. [PMID: 34878610 DOI: 10.1007/s00792-021-01252-x] [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: 07/03/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022]
Abstract
Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.
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Prediction of Genes That Function in Methanogenesis and CO 2 Pathways in Extremophiles. Microorganisms 2021; 9:microorganisms9112211. [PMID: 34835337 PMCID: PMC8621995 DOI: 10.3390/microorganisms9112211] [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] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.
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Tee HS, Waite D, Lear G, Handley KM. Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling. MICROBIOME 2021; 9:190. [PMID: 34544488 PMCID: PMC8454136 DOI: 10.1186/s40168-021-01145-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/02/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling. RESULTS Taxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively. CONCLUSIONS Our study demonstrates clear freshwater-saline and sediment-water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems. Video abstract.
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Affiliation(s)
- Hwee Sze Tee
- School of Biological Sciences, University of Auckland, Auckland, 1010 New Zealand
| | - David Waite
- School of Biological Sciences, University of Auckland, Auckland, 1010 New Zealand
- Current address: Ministry for Primary Industries, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, 1010 New Zealand
| | - Kim Marie Handley
- School of Biological Sciences, University of Auckland, Auckland, 1010 New Zealand
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López-Martínez VG, Guerrero-Álvarez JA, Ronderos-Lara JG, Murillo-Tovar MA, Solá-Pérez JE, León-Rivera I, Saldarriaga-Noreña H. Spectral Characteristics Related to Chemical Substructures and Structures Indicative of Organic Precursors from Fulvic Acids in Sediments by NMR and HPLC-ESI-MS. Molecules 2021; 26:molecules26134051. [PMID: 34279390 PMCID: PMC8272027 DOI: 10.3390/molecules26134051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to determine Fulvic Acids (FAs) in sediments to better know their composition at the molecular level and to propose substructures and structures of organic precursors. The sediment samples were obtained from a priority area for the conservation of ecosystems and biodiversity in Mexico. FAs were extracted and purified using modifications to the International Humic Substances Society method. The characterization was carried out by 1D and 2D nuclear magnetic resonance (NMR) and high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) in positive (ESI+) and negative (ESI−) modes. Twelve substructures were proposed by the COSY and HSQC experiments, correlating with compounds likely belonging to lignin derivatives obtained from soils as previously reported. The analysis of spectra obtained by HPLC-ESI-MS indicated likely presence of compounds chemically similar to that of the substructures elucidated by NMR. FAs studied are mainly constituted by carboxylic acids, hydroxyl, esters, vinyls, aliphatics, substituted aromatic rings, and amines, presenting structures related to organic precursors, such as lignin derivatives and polysaccharides.
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Affiliation(s)
- Verónica Gisela López-Martínez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Jorge A. Guerrero-Álvarez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - José Gustavo Ronderos-Lara
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Mario Alfonso Murillo-Tovar
- CONACYT-Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62290, Morelos, Mexico;
| | - Jorge Ernesto Solá-Pérez
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburna de Hidalgo Inn, Merida C.P. 97203, Yucatán, Mexico;
| | - Ismael León-Rivera
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
| | - Hugo Saldarriaga-Noreña
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca C.P. 62209, Morelos, Mexico; (V.G.L.-M.); (J.A.G.-Á.); (J.G.R.-L.); (I.L.-R.)
- Correspondence:
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10
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Wang B, Huang J, Yang J, Jiang H, Xiao H, Han J, Zhang X. Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments. FEMS Microbiol Ecol 2021; 97:6149456. [PMID: 33629724 DOI: 10.1093/femsec/fiab037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/23/2021] [Indexed: 11/12/2022] Open
Abstract
There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35-25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.
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Affiliation(s)
- Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Haiyi Xiao
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jibin Han
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 81008, China
| | - Xiying Zhang
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 81008, China
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11
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Coutinho FH, von Meijenfeldt FAB, Walter JM, Haro-Moreno JM, Lopéz-Pérez M, van Verk MC, Thompson CC, Cosenza CAN, Appolinario L, Paranhos R, Cabral A, Dutilh BE, Thompson FL. Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142758. [PMID: 33183813 DOI: 10.1016/j.scitotenv.2020.142758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/18/2023]
Abstract
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands; Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - F A B von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - J M Walter
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M Lopéz-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M C van Verk
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - C A N Cosenza
- COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - L Appolinario
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Paranhos
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - A Cabral
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - B E Dutilh
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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12
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Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. MICROBIOME 2020; 8:163. [PMID: 33213521 PMCID: PMC7678222 DOI: 10.1186/s40168-020-00936-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. RESULTS Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. CONCLUSIONS These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance. Video Abstract.
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Affiliation(s)
- F H Coutinho
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain.
| | - P J Cabello-Yeves
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Gonzalez-Serrano
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - M López-Pérez
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - T I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - F Rodriguez-Valera
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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13
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Wang R, Xu SY, Zhang M, Ghulam A, Dai CL, Zheng P. Iron as electron donor for denitrification: The efficiency, toxicity and mechanism. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 194:110343. [PMID: 32151862 DOI: 10.1016/j.ecoenv.2020.110343] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
For the treatment of low C/N wastewaters, methanol or acetate is usually dosed as electron donor for denitrification but such organics makes the process costly. To decrease the cost, iron which is the fourth most abundant element in lithosphere is suggested as the substitution of methanol and acetate. The peak volumetric removal rate (VRR) of nitrate nitrogen in the ferrous iron-dependent nitrate removal (FeNiR) reactor was 0.70 ± 0.04 kg-N/(m3·d), and the corresponding removal efficiency was 98%. Iron showed toxicity to cells by decreasing the live cell amount (dropped 56%) and the live cell activity (dropped 70%). The toxicity of iron was mainly expressed by the formation of iron encrustation. From microbial community data analysis, heterotrophs (Paracocccus, Thauera and Azoarcus) faded away while the facultative chemolithotrophs (Hyphomicrobium and Anaerolineaceae_uncultured) dominated in the reactor after replacing acetate with ferrous iron in the influent. Through scanning electron microscope (SEM) and transmission electron microscope (TEM), two iron oxidation sites in FeNiR cells were observed and accordingly two FeNiR mechanisms were proposed: 1) extracellular FeNiR in which ferrous iron was bio-oxidized extracellularly; and 2) intracellular FeNiR in which ferrous iron was chemically oxidized in periplasm. Bio-oxidation (extracellular FeNiR) and chemical oxidation (intracellular FeNiR) of ferrous iron coexisted in FeNiR reactor, but the former one predominated. Comparing with the control group without electron donor in the influent, FeNiR reactor showed 2 times higher and stable nitrate removal rate, suggesting iron could be used as electron donor for denitrification. However, further research works are still needed for the practical application of FeNiR in wastewater treatment.
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Affiliation(s)
- Ru Wang
- Environmental and Municipal Engineering College, Xi'an Univerisity of Architecture and Technology, Xi'an, 710055, PR China.
| | - Shao-Yi Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
| | - Meng Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment Water Research Institute, Nanyang Technological University, Singapore, 637141, Singapore.
| | - Abbas Ghulam
- Department of Chemical Engineering and Technology, University of Gujrat, Gujrat, 50700, Pakistan.
| | - Chen-Lin Dai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
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14
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Vasquez‐Cardenas D, Meysman FJR, Boschker HTS. A Cross-System Comparison of Dark Carbon Fixation in Coastal Sediments. GLOBAL BIOGEOCHEMICAL CYCLES 2020; 34:e2019GB006298. [PMID: 32713991 PMCID: PMC7375125 DOI: 10.1029/2019gb006298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 01/09/2020] [Accepted: 01/24/2020] [Indexed: 05/22/2023]
Abstract
Dark carbon fixation (DCF) by chemoautotrophic microorganisms can sustain food webs in the seafloor by local production of organic matter independent of photosynthesis. The process has received considerable attention in deep sea systems, such as hydrothermal vents, but the regulation, depth distribution, and global importance of coastal sedimentary DCF have not been systematically investigated. Here we surveyed eight coastal sediments by means of stable isotope probing (13C-DIC) combined with bacterial biomarkers (phospholipid-derived fatty acids) and compiled additional rates from literature into a global database. DCF rates in coastal sediments range from 0.07 to 36.30 mmol C m-2 day-1, and there is a linear relation between DCF and water depth. The CO2 fixation ratio (DCF/CO2 respired) also shows a trend with water depth, decreasing from 0.09 in nearshore environments to 0.04 in continental shelf sediments. Five types of depth distributions of chemoautotrophic activity are identified based on the mode of pore water transport (advective, bioturbated, and diffusive) and the dominant pathway of microbial sulfur oxidation. Extrapolated to the global coastal ocean, we estimate a DCF rate of 0.04 to 0.06 Pg C year-1, which is less than previous estimates based on indirect measurements (0.15 Pg C year-1), but remains substantially higher than the global DCF rate at deep sea hydrothermal vents (0.001-0.002 Pg C year-1).
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Affiliation(s)
| | - Filip J. R. Meysman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Henricus T. S. Boschker
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- Department of BiologyUniversity of AntwerpAntwerpBelgium
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15
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Zhao Y, Liu P, Rui J, Cheng L, Wang Q, Liu X, Yuan Q. Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134316. [PMID: 31783464 DOI: 10.1016/j.scitotenv.2019.134316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m-2 d-1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO2-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.
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Affiliation(s)
- Yuan Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Junpeng Rui
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, China
| | - Qian Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
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16
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Reddy B, Pandey J, Dubey SK. Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga. Gene 2019; 704:31-41. [DOI: 10.1016/j.gene.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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17
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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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18
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Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. mBio 2018; 9:mBio.00916-18. [PMID: 30108167 PMCID: PMC6094481 DOI: 10.1128/mbio.00916-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community. Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.
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Large perturbations in CO 2 flux and subsequent chemosynthesis are induced in agricultural soil by the addition of elemental sulfur. Sci Rep 2017; 7:4732. [PMID: 28680102 PMCID: PMC5498539 DOI: 10.1038/s41598-017-04934-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/22/2017] [Indexed: 11/08/2022] Open
Abstract
The microbial contribution to soil organic matter has been shown to be much larger than previously thought and thus it plays a major role in carbon cycling. Among soil microorganisms, chemoautotrophs can fix CO2 without sunlight and can glean energy through the oxidation of reduced elements such as sulfur. Here we show that the addition of sulfur to soil results in an initial surge in production of CO2 through microbial respiration, followed by an order of magnitude increase in the capture of carbon from the atmosphere as elemental sulfur is oxidised to sulfate. Thiobacillus spp., take advantage of specific conditions to become the dominant chemoautotrophic group that consumes CO2. We discern the direct incorporation of atmospheric carbon into soil carbohydrate, protein and aliphatic compounds and differentiate these from existing biomass. These results suggest that chemoautotrophs can play a large role in carbon cycling and that this carbon is heavily influenced by land management practises.
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20
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Gomez-Saez GV, Pop Ristova P, Sievert SM, Elvert M, Hinrichs KU, Bühring SI. Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System. Front Microbiol 2017; 8:702. [PMID: 28484442 PMCID: PMC5399606 DOI: 10.3389/fmicb.2017.00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
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Affiliation(s)
- Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
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Boschker HTS, Vasquez-Cardenas D, Bolhuis H, Moerdijk-Poortvliet TWC, Moodley L. Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments. PLoS One 2014; 9:e101443. [PMID: 25003508 PMCID: PMC4086895 DOI: 10.1371/journal.pone.0101443] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/06/2014] [Indexed: 11/18/2022] Open
Abstract
Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m−2 d−1. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)−1, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.
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Affiliation(s)
- Henricus T. S. Boschker
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
- * E-mail:
| | - Diana Vasquez-Cardenas
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
| | | | - Leon Moodley
- Marine Environment Group, International Research Institute of Stavanger (IRIS), Randaberg, Norway
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