1
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Xiang Q, Stryhanyuk H, Schmidt M, Kümmel S, Richnow HH, Zhu YG, Cui L, Musat N. Stable isotopes and nanoSIMS single-cell imaging reveals soil plastisphere colonizers able to assimilate sulfamethoxazole. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124197. [PMID: 38782163 DOI: 10.1016/j.envpol.2024.124197] [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: 08/28/2023] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The presence and accumulation of both, plastics and antibiotics in soils may lead to the colonization, selection, and propagation of soil bacteria with certain metabolic traits, e.g., antibiotic resistance, in the plastisphere. However, the impact of plastic-antibiotic tandem on the soil ecosystem functioning, particularly on microbial function and metabolism remains currently unexplored. Herein, we investigated the competence of soil bacteria to colonize plastics and degrade 13C-labeled sulfamethoxazole (SMX). Using single-cell imaging, isotope tracers, soil respiration and SMX mineralization bulk measurements we show that microbial colonization of polyethylene (PE) and polystyrene (PS) surfaces takes place within the first 30 days of incubation. Morphologically diverse microorganisms were colonizing both plastic types, with a slight preference for PE substrate. CARD-FISH bacterial cell counts on PE and PS surfaces formed under SMX amendment ranged from 5.36 × 103 to 2.06 × 104, and 2.06 × 103 to 3.43 × 103 hybridized cells mm-2, respectively. Nano-scale Secondary Ion Mass Spectrometry measurements show that 13C enrichment was highest at 130 days with values up to 1.29 atom%, similar to those of the 13CO2 pool (up to 1.26 atom%, or 22.55 ‰). Independent Mann-Whitney U test showed a significant difference between the control plastisphere samples incubated without SMX and those in 13C-SMX incubations (P < 0.001). Our results provide direct evidence demonstrating, at single-cell level, the capacity of bacterial colonizers of plastics to assimilate 13C-SMX from contaminated soils. These findings expand our knowledge on the role of soil-seeded plastisphere microbiota in the ecological functioning of soils impacted by anthropogenic stressors.
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Affiliation(s)
- Qian Xiang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Niculina Musat
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany; Department of Biology, Section for Microbiology, Aarhus University, 8000, Aarhus C, Denmark.
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2
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Lu C, Chen G, Song W, Chen K, Hee C, Nikan M, Guagliardo P, Bennett CF, Seth P, Iyer KS, Young SG, Qi X, Jiang H. Tool to Resolve Distortions in Elemental and Isotopic Imaging. J Am Chem Soc 2024; 146:20221-20229. [PMID: 38985464 DOI: 10.1021/jacs.4c05384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Nanoscale secondary ion mass spectrometry (NanoSIMS) makes it possible to visualize elements and isotopes in a wide range of samples at a high resolution. However, the fidelity and quality of NanoSIMS images often suffer from distortions because of a requirement to acquire and integrate multiple image frames. We developed an optical flow-based algorithm tool, NanoSIMS Stabilizer, for all-channel postacquisition registration of images. The NanoSIMS Stabilizer effectively deals with the distortions and artifacts, resulting in a high-resolution visualization of isotope and element distribution. It is open source with an easy-to-use ImageJ plugin and is accompanied by a Python version with GPU acceleration.
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Affiliation(s)
- Chixiang Lu
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Gu Chen
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Wenxin Song
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
| | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Charmaine Hee
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Mehran Nikan
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - C Frank Bennett
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Punit Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | | | - Stephen G Young
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
- Human Genetics, University of California, Los Angeles, California 90095, United States
| | - Xiaojuan Qi
- Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Haibo Jiang
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
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3
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Vaksmaa A, Vielfaure H, Polerecky L, Kienhuis MVM, van der Meer MTJ, Pflüger T, Egger M, Niemann H. Biodegradation of polyethylene by the marine fungus Parengyodontium album. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:172819. [PMID: 38679106 DOI: 10.1016/j.scitotenv.2024.172819] [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: 11/14/2023] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Plastic pollution in the marine realm is a severe environmental problem. Nevertheless, plastic may also serve as a potential carbon and energy source for microbes, yet the contribution of marine microbes, especially marine fungi to plastic degradation is not well constrained. We isolated the fungus Parengyodontium album from floating plastic debris in the North Pacific Subtropical Gyre and measured fungal-mediated mineralization rates (conversion to CO2) of polyethylene (PE) by applying stable isotope probing assays with 13C-PE over 9 days of incubation. When the PE was pretreated with UV light, the biodegradation rate of the initially added PE was 0.044 %/day. Furthermore, we traced the incorporation of PE-derived 13C carbon into P. album biomass using nanoSIMS and fatty acid analysis. Despite the high mineralization rate of the UV-treated 13C-PE, incorporation of PE-derived 13C into fungal cells was minor, and 13C incorporation was not detectable for the non-treated PE. Together, our results reveal the potential of P. album to degrade PE in the marine environment and to mineralize it to CO2. However, the initial photodegradation of PE is crucial for P. album to metabolize the PE-derived carbon.
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Affiliation(s)
- A Vaksmaa
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, the Netherlands.
| | - H Vielfaure
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - L Polerecky
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, the Netherlands
| | - M V M Kienhuis
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, the Netherlands
| | - M T J van der Meer
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, the Netherlands
| | - T Pflüger
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - M Egger
- The Ocean Cleanup, Rotterdam, the Netherlands; Egger Research and Consulting, St. Gallen, Switzerland
| | - H Niemann
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, the Netherlands
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4
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Schorn S, Graf JS, Littmann S, Hach PF, Lavik G, Speth DR, Schubert CJ, Kuypers MMM, Milucka J. Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility. Nat Commun 2024; 15:5293. [PMID: 38906896 PMCID: PMC11192741 DOI: 10.1038/s41467-024-49602-5] [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: 09/18/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d-1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.
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Affiliation(s)
- Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Carsten J Schubert
- Department of Surface Waters, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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5
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Smets B, Boschker HTS, Wetherington MT, Lelong G, Hidalgo-Martinez S, Polerecky L, Nuyts G, De Wael K, Meysman FJR. Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria. Front Microbiol 2024; 15:1208033. [PMID: 38525072 PMCID: PMC10959288 DOI: 10.3389/fmicb.2024.1208033] [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: 04/18/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.
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Affiliation(s)
- Bent Smets
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henricus T. S. Boschker
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Maxwell T. Wetherington
- Materials Characterization Laboratory, Pennsylvania State University, State College, PA, United States
| | - Gérald Lelong
- Institut de Minéralogie, de Physique des Matériaux et Cosmochimie (IMPMC), Sorbonne Universités, France—Muséum National d’Histoire Naturelle, Paris, France
| | | | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Nuyts
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Karolien De Wael
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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6
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Achberger AM, Jones R, Jamieson J, Holmes CP, Schubotz F, Meyer NR, Dekas AE, Moriarty S, Reeves EP, Manthey A, Brünjes J, Fornari DJ, Tivey MK, Toner BM, Sylvan JB. Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity. Nat Microbiol 2024; 9:657-668. [PMID: 38287146 DOI: 10.1038/s41564-024-01599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024]
Abstract
Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of 14C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin-Benson-Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.
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Affiliation(s)
- Amanda M Achberger
- Department of Oceanography, Texas A&M University, College Station, Texas, USA.
| | - Rose Jones
- Department of Soil, Water and Climate, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - John Jamieson
- Department of Earth Sciences, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Charles P Holmes
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Nicolette R Meyer
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Sarah Moriarty
- Department of Earth Sciences, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Eoghan P Reeves
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Alex Manthey
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jonas Brünjes
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel J Fornari
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Margaret K Tivey
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Brandy M Toner
- Department of Soil, Water and Climate, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA.
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7
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Paris ER, Arandia-Gorostidi N, Klempay B, Bowman JS, Pontefract A, Elbon CE, Glass JB, Ingall ED, Doran PT, Som SM, Schmidt BE, Dekas AE. Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity. SCIENCE ADVANCES 2023; 9:eadj3594. [PMID: 38134283 PMCID: PMC10745694 DOI: 10.1126/sciadv.adj3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-aw brine (an MgCl2-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an aw limit for detectable anabolic activity of 0.540, which is beyond the currently accepted limit of life based on cell division. This work demonstrates the utility of single-cell, metabolism-based techniques for detecting active life and expands the potential habitable space on Earth and beyond.
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Affiliation(s)
- Emily R. Paris
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | | | - Benjamin Klempay
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
| | - Jeff S. Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, USA
| | | | - Claire E. Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ellery D. Ingall
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Peter T. Doran
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sanjoy M. Som
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Britney E. Schmidt
- Departments of Astronomy and Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Anne E. Dekas
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
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8
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Candry P, Chadwick GL, Caravajal-Arroyo JM, Lacoere T, Winkler MKH, Ganigué R, Orphan VJ, Rabaey K. Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities. THE ISME JOURNAL 2023; 17:2014-2022. [PMID: 37715042 PMCID: PMC10579388 DOI: 10.1038/s41396-023-01508-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.
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Affiliation(s)
- Pieter Candry
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - José Maria Caravajal-Arroyo
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tim Lacoere
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | | | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium.
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9
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Spataro S, Maco B, Escrig S, Jensen L, Polerecky L, Knott G, Meibom A, Schneider BL. Stable isotope labeling and ultra-high-resolution NanoSIMS imaging reveal alpha-synuclein-induced changes in neuronal metabolism in vivo. Acta Neuropathol Commun 2023; 11:157. [PMID: 37770947 PMCID: PMC10540389 DOI: 10.1186/s40478-023-01608-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 09/30/2023] Open
Abstract
In Parkinson's disease, pathogenic factors such as the intraneuronal accumulation of the protein α-synuclein affect key metabolic processes. New approaches are required to understand how metabolic dysregulations cause degeneration of vulnerable subtypes of neurons in the brain. Here, we apply correlative electron microscopy and NanoSIMS isotopic imaging to map and quantify 13C enrichments in dopaminergic neurons at the subcellular level after pulse-chase administration of 13C-labeled glucose. To model a condition leading to neurodegeneration in Parkinson's disease, human α-synuclein was unilaterally overexpressed in the substantia nigra of one brain hemisphere in rats. When comparing neurons overexpressing α-synuclein to those located in the control hemisphere, the carbon anabolism and turnover rates revealed metabolic anomalies in specific neuronal compartments and organelles. Overexpression of α-synuclein enhanced the overall carbon turnover in nigral neurons, despite a lower relative incorporation of carbon inside the nucleus. Furthermore, mitochondria and Golgi apparatus showed metabolic defects consistent with the effects of α-synuclein on inter-organellar communication. By revealing changes in the kinetics of carbon anabolism and turnover at the subcellular level, this approach can be used to explore how neurodegeneration unfolds in specific subpopulations of neurons.
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Affiliation(s)
- Sofia Spataro
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bohumil Maco
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Louise Jensen
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lubos Polerecky
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Graham Knott
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Bioelectron Microscopy Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland.
- EPFL ENAC IIE LGB, Station 2, 1015, Lausanne, Switzerland.
| | - Bernard L Schneider
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Bertarelli Platform for Gene Therapy, Ecole Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland.
- EPFL SV PTECH PTBTG, Ch. Des Mines 9, 1202, Geneva, Switzerland.
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10
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Vaksmaa A, Polerecky L, Dombrowski N, Kienhuis MVM, Posthuma I, Gerritse J, Boekhout T, Niemann H. Polyethylene degradation and assimilation by the marine yeast Rhodotorula mucilaginosa. ISME COMMUNICATIONS 2023; 3:68. [PMID: 37423910 PMCID: PMC10330194 DOI: 10.1038/s43705-023-00267-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023]
Abstract
Ocean plastic pollution is a severe environmental problem but most of the plastic that has been released to the ocean since the 1950s is unaccounted for. Although fungal degradation of marine plastics has been suggested as a potential sink mechanism, unambiguous proof of plastic degradation by marine fungi, or other microbes, is scarce. Here we applied stable isotope tracing assays with 13C-labeled polyethylene to measure biodegradation rates and to trace the incorporation of plastic-derived carbon into individual cells of the yeast Rhodotorula mucilaginosa, which we isolated from the marine environment. 13C accumulation in the CO2 pool during 5-day incubation experiments with R. mucilaginosa and UV-irradiated 13C-labeled polyethylene as a sole energy and carbon source translated to degradation rates of 3.8% yr-1 of the initially added substrate. Furthermore, nanoSIMS measurements revealed substantial incorporation of polyethylene-derived carbon into fungal biomass. Our results demonstrate the potential of R. mucilaginosa to mineralize and assimilate carbon from plastics and suggest that fungal plastic degradation may be an important sink for polyethylene litter in the marine environment.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands.
| | - Lubos Polerecky
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Michiel V M Kienhuis
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Ilsa Posthuma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Jan Gerritse
- Deltares, Unit Subsurface and Groundwater Systems, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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11
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Arandia-Gorostidi N, Parada AE, Dekas AE. Single-cell view of deep-sea microbial activity and intracommunity heterogeneity. THE ISME JOURNAL 2023; 17:59-69. [PMID: 36202927 PMCID: PMC9750969 DOI: 10.1038/s41396-022-01324-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.
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Affiliation(s)
| | - A E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - A E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA.
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12
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Zhou Q, Tu C, Liu Y, Li Y, Zhang H, Vogts A, Plewe S, Pan X, Luo Y, Waniek JJ. Biofilm enhances the copper (II) adsorption on microplastic surfaces in coastal seawater: Simultaneous evidence from visualization and quantification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158217. [PMID: 36028022 DOI: 10.1016/j.scitotenv.2022.158217] [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: 05/29/2022] [Revised: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs) exposed to the urban coastal seawater could form biofilms, which facilitate the adsorption and transportation of hazardous contaminants. However, influence of biofilms on the metal adsorption of MPs, especially the co-existence of biofilm and metals on MPs, is still less known. In this study, the adsorption of copper (Cu) on biofilm-coated MPs (BMPs) was visually analyzed and quantified. The results of scanning electron microscopy in combination with energy dispersive X-ray showed that biofilm and metals co-occurred on MPs in seawater. The nanoscale secondary ion mass spectrometry images further exhibited that the distribution of Cu, chlorine (Cl) and biofilm on MP surfaces was highly consistent. Moreover, the adsorption of Cu(II) on BMPs was enhanced as quantified by inductively coupled plasma-mass spectrometer. Furthermore, different species on BMPs with and without Cu were identified, and their potential functions of metal or Cl metabolism were predicted based on KEGG pathway database. Overall, for the first time, this study provides visual and quantified evidences for the enhancement of Cu(II) adsorption on BMPs based on co-localization, and it may shed a light on the development of methodologies for investigating the interaction among MPs, biofilms and pollutants in marine environment.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; Leibniz Institute for Baltic Sea Research, Rostock 18119, Germany; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Chen Tu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Leibniz Institute for Baltic Sea Research, Rostock 18119, Germany; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Ying Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yuan Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Haibo Zhang
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research, Rostock 18119, Germany
| | - Sascha Plewe
- Leibniz Institute for Baltic Sea Research, Rostock 18119, Germany
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Joanna J Waniek
- Leibniz Institute for Baltic Sea Research, Rostock 18119, Germany
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13
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Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem. Nat Microbiol 2022; 7:2089-2100. [PMID: 36329197 DOI: 10.1038/s41564-022-01252-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using 13C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.
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14
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Intracellular development and impact of a marine eukaryotic parasite on its zombified microalgal host. THE ISME JOURNAL 2022; 16:2348-2359. [PMID: 35804051 PMCID: PMC9478091 DOI: 10.1038/s41396-022-01274-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022]
Abstract
Parasites are widespread and diverse in oceanic plankton and many of them infect single-celled algae for survival. How these parasites develop and scavenge energy within the host and how the cellular organization and metabolism of the host is altered remain open questions. Combining quantitative structural and chemical imaging with time-resolved transcriptomics, we unveil dramatic morphological and metabolic changes of the marine parasite Amoebophrya (Syndiniales) during intracellular infection, particularly following engulfment and digestion of nutrient-rich host chromosomes. Changes include a sequential acristate and cristate mitochondrion with a 200-fold increase in volume, a 13-fold increase in nucleus volume, development of Golgi apparatus and a metabolic switch from glycolysis (within the host) to TCA (free-living dinospore). Similar changes are seen in apicomplexan parasites, thus underlining convergent traits driven by metabolic constraints and the infection cycle. In the algal host, energy-producing organelles (plastid, mitochondria) remain relatively intact during most of the infection. We also observed that sugar reserves diminish while lipid droplets increase. Rapid infection of the host nucleus could be a “zombifying” strategy, allowing the parasite to digest nutrient-rich chromosomes and escape cytoplasmic defense, whilst benefiting from maintained carbon-energy production of the host cell.
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15
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Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. THE ISME JOURNAL 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
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Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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16
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Arandia-Gorostidi N, Berthelot H, Calabrese F, Stryhanyuk H, Klawonn I, Iversen M, Nahar N, Grossart HP, Ploug H, Musat N. Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups. Sci Rep 2022; 12:14949. [PMID: 36056039 PMCID: PMC9440002 DOI: 10.1038/s41598-022-18915-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of 13C and 15N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in 13C and 15N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318, Leipzig, Germany.
- Department of Earth System Science, Stanford University, Green Earth Sciences Building, 367 Panama St., Room 129, Stanford, CA, 94305-4216, USA.
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Hugo Berthelot
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318, Leipzig, Germany
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France
- IFREMER, DYNECO, Pelagos Laboratory, Plouzané, France
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318, Leipzig, Germany
- Department of Organismic and Evolutionary BiologyBiological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA, USA
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318, Leipzig, Germany
| | - Isabell Klawonn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691, Stockholm, Sweden
- Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Morten Iversen
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Marum and University of Bremen, Bremen, Germany
| | - Nurun Nahar
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
- Department Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin/Stechlin, Germany
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318, Leipzig, Germany.
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17
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Munds RA, Cooper EB, Janiak MC, Lam LG, DeCasien AR, Bauman Surratt S, Montague MJ, Martinez MI, Research Unit CB, Kawamura S, Higham JP, Melin AD. Variation and heritability of retinal cone ratios in a free-ranging population of rhesus macaques. Evolution 2022; 76:1776-1789. [PMID: 35790204 PMCID: PMC9544366 DOI: 10.1111/evo.14552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 01/22/2023]
Abstract
A defining feature of catarrhine primates is uniform trichromacy-the ability to distinguish red (long; L), green (medium; M), and blue (short; S) wavelengths of light. Although the tuning of photoreceptors is conserved, the ratio of L:M cones in the retina is variable within and between species, with human cone ratios differing from other catarrhines. Yet, the sources and structure of variation in cone ratios are poorly understood, precluding a broader understanding of color vision variability. Here, we report a large-scale study of a pedigreed population of rhesus macaques (Macaca mulatta). We collected foveal RNA and analyzed opsin gene expression using cDNA and estimated additive genetic variance of cone ratios. The average L:M ratio and standard error was 1.03:1 ± 0.02. There was no age effect, and genetic contribution to variation was negligible. We found marginal sex effects with females having larger ratios than males. S cone ratios (0.143:1 ± 0.002) had significant genetic variance with a heritability estimate of 43% but did not differ between sexes or age groups. Our results contextualize the derived human condition of L-cone dominance and provide new information about the heritability of cone ratios and variation in primate color vision.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABT2N 1N4Canada
| | - Eve B. Cooper
- Department of AnthropologyNew York UniversityNew YorkNew York10003,New York Consortium in Evolutionary PrimatologyNew YorkNew York10460
| | - Mareike C. Janiak
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABT2N 1N4Canada,Department of AnthropologyNew York UniversityNew YorkNew York10003,School of Science, Engineering and EnvironmentUniversity of SalfordSalfordM5 4NTUnited Kingdom
| | - Linh Gia Lam
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABT2N 1N4Canada
| | - Alex R. DeCasien
- Department of AnthropologyNew York UniversityNew YorkNew York10003,New York Consortium in Evolutionary PrimatologyNew YorkNew York10460,Section on Developmental NeurogenomicsNational Institute of Mental HealthBethesdaMaryland20892
| | | | - Michael J. Montague
- Department of NeuroscienceUniversity of PennsylvaniaPhiladelphiaPennsylvania19104
| | - Melween I. Martinez
- Caribbean Primate Research CenterUniversity of Puerto RicoSan JuanPuerto Rico00936
| | | | - Shoji Kawamura
- Department of Integrated BiosciencesUniversity of TokyoKashiwa277‐8562Japan
| | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew York10003,New York Consortium in Evolutionary PrimatologyNew YorkNew York10460
| | - Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABT2N 1N4Canada,Department of Medical GeneticsUniversity of CalgaryCalgaryABT2N 1N4Canada,Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryABT2N 1N4Canada
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18
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Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX. Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Curr Biol 2022; 32:3059-3069.e7. [PMID: 35777363 PMCID: PMC9496226 DOI: 10.1016/j.cub.2022.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.
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Affiliation(s)
- Julia A Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Benjamin R K Roller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Center for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria; Department of Environmental Systems Sciences, ETH Zürich, Universitätsstrasse 16, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Ueberlandstrasse 133, Dübendorf 8600, Switzerland
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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19
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Klotz F, Kitzinger K, Ngugi DK, Büsing P, Littmann S, Kuypers MMM, Schink B, Pester M. Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels. THE ISME JOURNAL 2022; 16:1647-1656. [PMID: 35260828 PMCID: PMC9122916 DOI: 10.1038/s41396-022-01216-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 05/09/2023]
Abstract
Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1, corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell-1 d-1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 109 g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.
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Affiliation(s)
- Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - David Kamanda Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, D-78457, Germany.
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, D-38124, Braunschweig, Germany.
- Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, D-38106, Braunschweig, Germany.
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20
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Geerlings NMJ, Kienhuis MVM, Hidalgo-Martinez S, Hageman R, Vasquez-Cardenas D, Middelburg JJ, Meysman FJR, Polerecky L. Polyphosphate Dynamics in Cable Bacteria. Front Microbiol 2022; 13:883807. [PMID: 35663875 PMCID: PMC9159916 DOI: 10.3389/fmicb.2022.883807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
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Affiliation(s)
- Nicole M. J. Geerlings
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nicole M. J. Geerlings,
| | | | - Silvia Hidalgo-Martinez
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Renee Hageman
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Diana Vasquez-Cardenas
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | | | - Filip J. R. Meysman
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- Lubos Polerecky,
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21
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Eigemann F, Rahav E, Grossart HP, Aharonovich D, Sher D, Vogts A, Voss M. Phytoplankton exudates provide full nutrition to a subset of accompanying heterotrophic bacteria via carbon, nitrogen and phosphorus allocation. Environ Microbiol 2022; 24:2467-2483. [PMID: 35146867 DOI: 10.1111/1462-2920.15933] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
Marine bacteria rely on phytoplankton exudates as carbon sources (DOCp). Yet, it is unclear to what extent phytoplankton exudates also provide nutrients such as phytoplankton-derived N and P (DONp, DOPp). We address these questions by mesocosm exudate addition experiments with spent media from the ubiquitous pico-cyanobacterium Prochlorococcus to bacterial communities in contrasting ecosystems in the Eastern Mediterranean - a coastal and an open-ocean, oligotrophic station with and without on-top additions of inorganic nutrients. Inorganic nutrient addition did not lower the incorporation of exudate DONp, nor did it reduce alkaline phosphatase activity, suggesting that bacterial communities are able to exclusively cover their nitrogen and phosphorus demands with organic forms provided by phytoplankton exudates. Approximately half of the cells in each ecosystem took up detectable amounts of Prochlorococcus-derived C and N, yet based on 16S rRNA sequencing different bacterial genera were responsible for the observed exudate utilization patterns. In the coastal community, several phylotypes of Aureimarina, Psychrosphaera and Glaciecola responded positively to the addition of phytoplankton exudates, whereas phylotypes of Pseudoalteromonas increased and dominated the open-ocean communities. Together, our results strongly indicate that phytoplankton exudates provide coastal and open-ocean bacterial communities with organic carbon, nitrogen and phosphorus, and that phytoplankton exudate serve a full-fledged meal for the accompanying bacterial community in the nutrient-poor eastern Mediterranean. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Falk Eigemann
- Leibniz-Institute for Baltic Sea Research Warnemünde.,Water quality engineering, Technical University of Berlin
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa
| | | | | | - Daniel Sher
- Leon H. Charney School of Marine Sciences, University Haifa
| | - Angela Vogts
- Leibniz-Institute for Baltic Sea Research Warnemünde
| | - Maren Voss
- Leibniz-Institute for Baltic Sea Research Warnemünde
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22
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Foster RA, Tienken D, Littmann S, Whitehouse MJ, Kuypers MMM, White AE. The rate and fate of N 2 and C fixation by marine diatom-diazotroph symbioses. THE ISME JOURNAL 2022; 16:477-487. [PMID: 34429522 PMCID: PMC8776783 DOI: 10.1038/s41396-021-01086-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 11/08/2022]
Abstract
N2 fixation constitutes an important new nitrogen source in the open sea. One group of filamentous N2 fixing cyanobacteria (Richelia intracellularis, hereafter Richelia) form symbiosis with a few genera of diatoms. High rates of N2 fixation and carbon (C) fixation have been measured in the presence of diatom-Richelia symbioses. However, it is unknown how partners coordinate C fixation and how the symbiont sustains high rates of N2 fixation. Here, both the N2 and C fixation in wild diatom-Richelia populations are reported. Inhibitor experiments designed to inhibit host photosynthesis, resulted in lower estimated growth and depressed C and N2 fixation, suggesting that despite the symbionts ability to fix their own C, they must still rely on their respective hosts for C. Single cell analysis indicated that up to 22% of assimilated C in the symbiont is derived from the host, whereas 78-91% of the host N is supplied from their symbionts. A size-dependent relationship is identified where larger cells have higher N2 and C fixation, and only N2 fixation was light dependent. Using the single cell measures, the N-rich phycosphere surrounding these symbioses was estimated and contributes directly and rapidly to the surface ocean rather than the mesopelagic, even at high estimated sinking velocities (<10 m d-1). Several eco-physiological parameters necessary for incorporating symbiotic N2 fixing populations into larger basin scale biogeochemical models (i.e., N and C cycles) are provided.
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Affiliation(s)
- Rachel A Foster
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
| | - Daniela Tienken
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin J Whitehouse
- Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Angelicque E White
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
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23
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Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. THE ISME JOURNAL 2022; 16:168-177. [PMID: 34285362 PMCID: PMC8692474 DOI: 10.1038/s41396-021-01047-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.
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24
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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25
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Mohr W, Lehnen N, Ahmerkamp S, Marchant HK, Graf JS, Tschitschko B, Yilmaz P, Littmann S, Gruber-Vodicka H, Leisch N, Weber M, Lott C, Schubert CJ, Milucka J, Kuypers MMM. Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium. Nature 2021; 600:105-109. [PMID: 34732889 PMCID: PMC8636270 DOI: 10.1038/s41586-021-04063-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/22/2021] [Indexed: 01/23/2023]
Abstract
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1-3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate symbioses are lacking for seagrasses, which evolved around 100 million years ago from terrestrial flowering plants that migrated back to the sea5. Here we describe an N2-fixing symbiont, 'Candidatus Celerinatantimonas neptuna', that lives inside seagrass root tissue, where it provides ammonia and amino acids to its host in exchange for sugars. As such, this symbiosis is reminiscent of terrestrial N2-fixing plant symbioses. The symbiosis between Ca. C. neptuna and its host Posidonia oceanica enables highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea. Relatives of Ca. C. neptuna occur worldwide in coastal ecosystems, in which they may form similar symbioses with other seagrasses and saltmarsh plants. Just like N2-fixing microorganisms might have aided the colonization of nitrogen-poor soils by early land plants6, the ancestors of Ca. C. neptuna and its relatives probably enabled flowering plants to invade nitrogen-poor marine habitats, where they formed extremely efficient blue carbon ecosystems7.
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Affiliation(s)
- Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Nadine Lehnen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Data Science Research Group, Institute for Artificial Intelligence in Medicine, University Hospital Essen, Essen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | - Carsten J Schubert
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Department of Surface Waters-Research and Management, Kastanienbaum, Switzerland
| | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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26
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Sun H, Jiang S, Jiang C, Wu C, Gao M, Wang Q. A review of root exudates and rhizosphere microbiome for crop production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54497-54510. [PMID: 34431053 DOI: 10.1007/s11356-021-15838-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/02/2021] [Indexed: 05/04/2023]
Abstract
Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.
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Affiliation(s)
- Haishu Sun
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chuanfu Wu
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Ming Gao
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Qunhui Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China.
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27
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Decelle J, Veronesi G, LeKieffre C, Gallet B, Chevalier F, Stryhanyuk H, Marro S, Ravanel S, Tucoulou R, Schieber N, Finazzi G, Schwab Y, Musat N. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae. Environ Microbiol 2021; 23:6569-6586. [PMID: 34499794 DOI: 10.1111/1462-2920.15766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022]
Abstract
Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium). We showed that this symbiosis is very dynamic whereby symbionts interact with different host cells via extracellular vesicles within the colony. 3D electron microscopy revealed that the photosynthetic apparatus of the microalgae was more voluminous in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were stored in the symbiotic microalga in starch granules and purine crystals respectively. Nitrogen was also allocated to the algal nucleolus. In the host, low 13 C transfer was detected in the Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (c. 40 ppm) and twofold higher in the host, whereas copper concentration increased in symbionts and was detected in the host cell and extracellular vesicles. Sulfur concentration was around two times higher in symbionts (chromatin and pyrenoid) than their host. This study improves our understanding on the functioning of this oceanic photosymbiosis and paves the way for more studies to further assess its biogeochemical significance.
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Affiliation(s)
- Johan Decelle
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France.,Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Giulia Veronesi
- CNRS, Laboratoire de Chimie et Biologie des Métaux (LCBM), UMR 5249 CNRS-CEA-UGA, F-38054, Grenoble, France.,CEA, LCBM, F-38054, Grenoble, France.,Université Grenoble Alpes, LCBM, F-38054, Grenoble, France.,ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | | | - Benoit Gallet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Fabien Chevalier
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sophie Marro
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), UMR 7093, Observatoire Océanologique, 06230, Villefranche-sur-Mer, France
| | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Rémi Tucoulou
- ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | - Nicole Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Giovanni Finazzi
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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28
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Calabrese F, Stryhanyuk H, Moraru C, Schlömann M, Wick LY, Richnow HH, Musat F, Musat N. Metabolic history and metabolic fitness as drivers of anabolic heterogeneity in isogenic microbial populations. Environ Microbiol 2021; 23:6764-6776. [PMID: 34472201 DOI: 10.1111/1462-2920.15756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behaviour. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time-resolved stable isotope probing and nanoscale secondary ion mass spectrometry to quantify substrate assimilation by individual cells of Pseudomonas putida, P. stutzeri and Thauera aromatica. Acetate and benzoate at different concentrations were used as substrates. Anabolic heterogeneity was quantified by the cumulative differentiation tendency index. We observed two major, opposing trends of anabolic heterogeneity over time. Most often, microbial populations started as highly heterogeneous, with heterogeneity decreasing by various degrees over time. The second, less frequently observed trend, saw microbial populations starting at low or very low heterogeneity, and remaining largely stable over time. We explain these trends as an interplay of metabolic history (e.g. former growth substrate or other nutrient limitations) and metabolic fitness (i.e. the fine-tuning of metabolic pathways to process a defined growth substrate). Our results offer a new viewpoint on the intra-population functional diversification often encountered in the environment, and suggests that some microbial populations may be intrinsically heterogeneous.
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Affiliation(s)
- Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Schlömann
- Department of Environmental Microbiology, Institute of Biosciences, TU-Bergakademie Freiberg, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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29
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Turk-Kubo KA, Mills MM, Arrigo KR, van Dijken G, Henke BA, Stewart B, Wilson ST, Zehr JP. UCYN-A/haptophyte symbioses dominate N 2 fixation in the Southern California Current System. ISME COMMUNICATIONS 2021; 1:42. [PMID: 36740625 PMCID: PMC9723760 DOI: 10.1038/s43705-021-00039-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
The availability of fixed nitrogen (N) is an important factor limiting biological productivity in the oceans. In coastal waters, high dissolved inorganic N concentrations were historically thought to inhibit dinitrogen (N2) fixation, however, recent N2 fixation measurements and the presence of the N2-fixing UCYN-A/haptophyte symbiosis in nearshore waters challenge this paradigm. We characterized the contribution of UCYN-A symbioses to nearshore N2 fixation in the Southern California Current System (SCCS) by measuring bulk community and single-cell N2 fixation rates, as well as diazotroph community composition and abundance. UCYN-A1 and UCYN-A2 symbioses dominated diazotroph communities throughout the region during upwelling and oceanic seasons. Bulk N2 fixation was detected in most surface samples, with rates up to 23.0 ± 3.8 nmol N l-1 d-1, and was often detected at the deep chlorophyll maximum in the presence of nitrate (>1 µM). UCYN-A2 symbiosis N2 fixation rates were higher (151.1 ± 112.7 fmol N cell-1 d-1) than the UCYN-A1 symbiosis (6.6 ± 8.8 fmol N cell-1 d-1). N2 fixation by the UCYN-A1 symbiosis accounted for a majority of the measured bulk rates at two offshore stations, while the UCYN-A2 symbiosis was an important contributor in three nearshore stations. This report of active UCYN-A symbioses and broad mesoscale distribution patterns establishes UCYN-A symbioses as the dominant diazotrophs in the SCCS, where heterocyst-forming and unicellular cyanobacteria are less prevalent, and provides evidence that the two dominant UCYN-A sublineages are separate ecotypes.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA.
| | - Matthew M Mills
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Kevin R Arrigo
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Gert van Dijken
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Britt A Henke
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Brittany Stewart
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Samuel T Wilson
- Center for Microbial Oceanography: Research and Education, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
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30
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Duerschlag J, Mohr W, Ferdelman TG, LaRoche J, Desai D, Croot PL, Voß D, Zielinski O, Lavik G, Littmann S, Martínez-Pérez C, Tschitschko B, Bartlau N, Osterholz H, Dittmar T, Kuypers MMM. Niche partitioning by photosynthetic plankton as a driver of CO 2-fixation across the oligotrophic South Pacific Subtropical Ocean. ISME JOURNAL 2021; 16:465-476. [PMID: 34413475 PMCID: PMC8776750 DOI: 10.1038/s41396-021-01072-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022]
Abstract
Oligotrophic ocean gyre ecosystems may be expanding due to rising global temperatures [1-5]. Models predicting carbon flow through these changing ecosystems require accurate descriptions of phytoplankton communities and their metabolic activities [6]. We therefore measured distributions and activities of cyanobacteria and small photosynthetic eukaryotes throughout the euphotic zone on a zonal transect through the South Pacific Ocean, focusing on the ultraoligotrophic waters of the South Pacific Gyre (SPG). Bulk rates of CO2 fixation were low (0.1 µmol C l-1 d-1) but pervasive throughout both the surface mixed-layer (upper 150 m), as well as the deep chlorophyll a maximum of the core SPG. Chloroplast 16S rRNA metabarcoding, and single-cell 13CO2 uptake experiments demonstrated niche differentiation among the small eukaryotes and picocyanobacteria. Prochlorococcus abundances, activity, and growth were more closely associated with the rims of the gyre. Small, fast-growing, photosynthetic eukaryotes, likely related to the Pelagophyceae, characterized the deep chlorophyll a maximum. In contrast, a slower growing population of photosynthetic eukaryotes, likely comprised of Dictyochophyceae and Chrysophyceae, dominated the mixed layer that contributed 65-88% of the areal CO2 fixation within the core SPG. Small photosynthetic eukaryotes may thus play an underappreciated role in CO2 fixation in the surface mixed-layer waters of ultraoligotrophic ecosystems.
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Affiliation(s)
- Julia Duerschlag
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Peter L Croot
- iCRAG (Irish Centre for Research in Applied Geoscience), Earth and Ocean Sciences, School of Natural Sciences and the Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Daniela Voß
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Oliver Zielinski
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Marine Perception Research Group, German Research Center for Artificial Intelligence (DFKI), Oldenburg, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Clara Martínez-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | | | - Nina Bartlau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
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31
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Evidence of a Streamlined Extracellular Electron Transfer Pathway from Biofilm Structure, Metabolic Stratification, and Long-Range Electron Transfer Parameters. Appl Environ Microbiol 2021; 87:e0070621. [PMID: 34190605 PMCID: PMC8357294 DOI: 10.1128/aem.00706-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A strain of Geobacter sulfurreducens, an organism capable of respiring solid extracellular substrates, lacking four of five outer membrane cytochrome complexes (extABCD+ strain) grows faster and produces greater current density than the wild type grown under identical conditions. To understand cellular and biofilm modifications in the extABCD+ strain responsible for this increased performance, biofilms grown using electrodes as terminal electron acceptors were sectioned and imaged using electron microscopy to determine changes in thickness and cell density, while parallel biofilms incubated in the presence of nitrogen and carbon isotopes were analyzed using NanoSIMS (nanoscale secondary ion mass spectrometry) to quantify and localize anabolic activity. Long-distance electron transfer parameters were measured for wild-type and extABCD+ biofilms spanning 5-μm gaps. Our results reveal that extABCD+ biofilms achieved higher current densities through the additive effects of denser cell packing close to the electrode (based on electron microscopy), combined with higher metabolic rates per cell compared to the wild type (based on increased rates of 15N incorporation). We also observed an increased rate of electron transfer through extABCD+ versus wild-type biofilms, suggesting that denser biofilms resulting from the deletion of unnecessary multiheme cytochromes streamline electron transfer to electrodes. The combination of imaging, physiological, and electrochemical data confirms that engineered electrogenic bacteria are capable of producing more current per cell and, in combination with higher biofilm density and electron diffusion rates, can produce a higher final current density than the wild type. IMPORTANCE Current-producing biofilms in microbial electrochemical systems could potentially sustain technologies ranging from wastewater treatment to bioproduction of electricity if the maximum current produced could be increased and current production start-up times after inoculation could be reduced. Enhancing the current output of microbial electrochemical systems has been mostly approached by engineering physical components of reactors and electrodes. Here, we show that biofilms formed by a Geobacter sulfurreducens strain producing ∼1.4× higher current than the wild type results from a combination of denser cell packing and higher anabolic activity, enabled by an increased rate of electron diffusion through the biofilms. Our results confirm that it is possible to engineer electrode-specific G. sulfurreducens strains with both faster growth on electrodes and streamlined electron transfer pathways for enhanced current production.
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32
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Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, Marchant HK, Storelli N, Winkel LHE, Schubert CJ, Mohr W, Kuypers MMM. Purple sulfur bacteria fix N 2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun 2021; 12:4774. [PMID: 34362886 PMCID: PMC8346585 DOI: 10.1038/s41467-021-25000-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.
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Affiliation(s)
- Miriam Philippi
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jasmine S Berg
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland
| | - Bernhard Tschitschko
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Abiel T Kidane
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Lenny H E Winkel
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
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33
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Gradoville MR, Cabello AM, Wilson ST, Turk-Kubo KA, Karl DM, Zehr JP. Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A. Environ Microbiol 2021; 23:4518-4531. [PMID: 34227720 PMCID: PMC9291983 DOI: 10.1111/1462-2920.15645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022]
Abstract
The symbiotic cyanobacterium UCYN‐A is one of the most globally abundant marine dinitrogen (N2)‐fixers, but cultures have not been available and its biology and ecology are poorly understood. We used cultivation‐independent approaches to investigate how UCYN‐A single‐cell N2 fixation rates (NFRs) and nifH gene expression vary as a function of depth and photoperiod. Twelve‐hour day/night incubations showed that UCYN‐A only fixed N2 during the day. Experiments conducted using in situ arrays showed a light‐dependence of NFRs by the UCYN‐A symbiosis, with the highest rates in surface waters (5–45 m) and lower rates at depth (≥ 75 m). Analysis of NFRs versus in situ light intensity yielded a light saturation parameter (Ik) for UCYN‐A of 44 μmol quanta m−2 s−1. This is low compared with other marine diazotrophs, suggesting an ecological advantage for the UCYN‐A symbiosis under low‐light conditions. In contrast to cell‐specific NFRs, nifH gene‐specific expression levels did not vary with depth, indicating that light regulates N2 fixation by UCYN‐A through processes other than transcription, likely including host–symbiont interactions. These results offer new insights into the physiology of the UCYN‐A symbiosis in the subtropical North Pacific Ocean and provide clues to the environmental drivers of its global distributions.
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Affiliation(s)
- Mary R Gradoville
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ana M Cabello
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.,Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain
| | - Samuel T Wilson
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David M Karl
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
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34
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Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae. Proc Natl Acad Sci U S A 2021; 118:2025252118. [PMID: 34215695 DOI: 10.1073/pnas.2025252118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.
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35
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Efficient long-range conduction in cable bacteria through nickel protein wires. Nat Commun 2021; 12:3996. [PMID: 34183682 PMCID: PMC8238962 DOI: 10.1038/s41467-021-24312-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Filamentous cable bacteria display long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating protein shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.
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36
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Chen SC, Budhraja R, Adrian L, Calabrese F, Stryhanyuk H, Musat N, Richnow HH, Duan GL, Zhu YG, Musat F. Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. ISME JOURNAL 2021; 15:3508-3521. [PMID: 34117322 PMCID: PMC8630052 DOI: 10.1038/s41396-021-01022-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 11/23/2022]
Abstract
Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of 13C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Rohit Budhraja
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China. .,Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021, Xiamen, China.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany.
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37
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Landa M, Turk-Kubo KA, Cornejo-Castillo FM, Henke BA, Zehr JP. Critical Role of Light in the Growth and Activity of the Marine N 2-Fixing UCYN-A Symbiosis. Front Microbiol 2021; 12:666739. [PMID: 34025621 PMCID: PMC8139342 DOI: 10.3389/fmicb.2021.666739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
The unicellular N2-fixing cyanobacteria UCYN-A live in symbiosis with haptophytes in the Braarudosphaera bigelowii lineage. Maintaining N2-fixing symbioses between two unicellular partners requires tight coordination of multiple biological processes including cell growth and division and, in the case of the UCYN-A symbiosis, N2 fixation of the symbiont and photosynthesis of the host. In this system, it is thought that the host photosynthesis supports the high energetic cost of N2 fixation, and both processes occur during the light period. However, information on this coordination is very limited and difficult to obtain because the UCYN-A symbiosis has yet to be available in culture. Natural populations containing the UCYN-A2 symbiosis were manipulated to explore the effects of alterations of regular light and dark periods and inhibition of host photosynthesis on N2 fixation (single cell N2 fixation rates), nifH gene transcription, and UCYN-A2 cell division (fluorescent in situ hybridization and nifH gene abundances). The results showed that the light period is critical for maintenance of regular patterns of gene expression, N2 fixation and symbiont replication and cell division. This study suggests a crucial role for the host as a producer of fixed carbon, rather than light itself, in the regulation and implementation of these cellular processes in UCYN-A.
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Affiliation(s)
- Marine Landa
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Britt A Henke
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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38
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Trembath-Reichert E, Shah Walter SR, Ortiz MAF, Carter PD, Girguis PR, Huber JA. Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids. SCIENCE ADVANCES 2021; 7:7/18/eabg0153. [PMID: 33910898 PMCID: PMC8081358 DOI: 10.1126/sciadv.abg0153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Abstract
Biogeochemical processes occurring in fluids that permeate oceanic crust make measurable contributions to the marine carbon cycle, but quantitative assessments of microbial impacts on this vast, subsurface carbon pool are lacking. We provide bulk and single-cell estimates of microbial biomass production from carbon and nitrogen substrates in cool, oxic basement fluids from the western flank of the Mid-Atlantic Ridge. The wide range in carbon and nitrogen incorporation rates indicates a microbial community well poised for dynamic conditions, potentially anabolizing carbon and nitrogen at rates ranging from those observed in subsurface sediments to those found in on-axis hydrothermal vent environments. Bicarbonate incorporation rates were highest where fluids are most isolated from recharging bottom seawater, suggesting that anabolism of inorganic carbon may be a potential strategy for supplementing the ancient and recalcitrant dissolved organic carbon that is prevalent in the globally distributed subseafloor crustal environment.
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Affiliation(s)
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
| | | | - Patrick D Carter
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Applied Ocean Engineering and Physics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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39
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Klempay B, Arandia-Gorostidi N, Dekas AE, Bartlett DH, Carr CE, Doran PT, Dutta A, Erazo N, Fisher LA, Glass JB, Pontefract A, Som SM, Wilson JM, Schmidt BE, Bowman JS. Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds. Environ Microbiol 2021; 23:3825-3839. [PMID: 33621409 DOI: 10.1111/1462-2920.15440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 01/02/2023]
Abstract
Concurrent osmotic and chaotropic stress make MgCl2 -rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl2 brines. Within NaCl brines, we observed a proliferation of specialized halophilic Euryarchaeota, which corresponded closely with the dominant taxa found in salterns around the world. These communities were characterized by very slow growth rates and high biomass accumulation. As salinity and chaotropicity increased, we found that the MgCl2 -rich brines eventually exceeded the limits of microbial activity. We found evidence that exogenous genetic material is preserved in these chaotropic brines, producing an unexpected increase in diversity in the presumably sterile MgCl2 -saturated brines. Because of their high potential for biomarker preservation, chaotropic brines could therefore serve as repositories of genetic biomarkers from nearby environments (both on Earth and beyond) making them prime targets for future life-detection missions.
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Affiliation(s)
- Benjamin Klempay
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | | | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Christopher E Carr
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Peter T Doran
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Avishek Dutta
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Natalia Erazo
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Luke A Fisher
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Sanjoy M Som
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA
| | - Jesse M Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Britney E Schmidt
- School of Earth and Atmospheric Studies, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
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40
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Polerecky L, Masuda T, Eichner M, Rabouille S, Vancová M, Kienhuis MVM, Bernát G, Bonomi-Barufi J, Campbell DA, Claquin P, Červený J, Giordano M, Kotabová E, Kromkamp J, Lombardi AT, Lukeš M, Prášil O, Stephan S, Suggett D, Zavřel T, Halsey KH. Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. Front Microbiol 2021; 12:620915. [PMID: 33613489 PMCID: PMC7890256 DOI: 10.3389/fmicb.2021.620915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/11/2021] [Indexed: 12/05/2022] Open
Abstract
Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilitate its success in dynamic aquatic environments.
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Affiliation(s)
- Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Takako Masuda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Meri Eichner
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, Villefranche-sur-mer, France
- Sorbonne Université, CNRS, Laboratoire d’Océanographie Microbienne, Banyuls-sur-mer, France
| | - Marie Vancová
- Institute of Parasitology, Czech Academy of Sciences, Biology Centre, České Budějovice, Czechia
| | | | - Gabor Bernát
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Centre for Ecological Research, Balaton Limnological Institute, Tihany, Hungary
| | - Jose Bonomi-Barufi
- Botany Department, Federal University of Santa Catarina, Campus de Trindade, Florianópolis, Brazil
| | | | - Pascal Claquin
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques, FRE 2030, Muséum National d’Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Normandie Université, Esplanade de la Paix, France
| | - Jan Červený
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Mario Giordano
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, College of Sciences, Shantou University, Shantou, China
| | - Eva Kotabová
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Jacco Kromkamp
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | | | - Martin Lukeš
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Ondrej Prášil
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Susanne Stephan
- Department Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Department of Ecology, Berlin Institute of Technology, Berlin, Germany
| | - David Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tomas Zavřel
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Metcalfe KS, Murali R, Mullin SW, Connon SA, Orphan VJ. Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy. THE ISME JOURNAL 2021; 15:377-396. [PMID: 33060828 PMCID: PMC8027057 DOI: 10.1038/s41396-020-00757-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/28/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023]
Abstract
Archaeal anaerobic methanotrophs ("ANME") and sulfate-reducing Deltaproteobacteria ("SRB") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b-SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b-SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.
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Affiliation(s)
- Kyle S Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
| | - Ranjani Murali
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
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Geerlings NMJ, Geelhoed JS, Vasquez-Cardenas D, Kienhuis MVM, Hidalgo-Martinez S, Boschker HTS, Middelburg JJ, Meysman FJR, Polerecky L. Cell Cycle, Filament Growth and Synchronized Cell Division in Multicellular Cable Bacteria. Front Microbiol 2021; 12:620807. [PMID: 33584623 PMCID: PMC7873302 DOI: 10.3389/fmicb.2021.620807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cable bacteria are multicellular, Gram-negative filamentous bacteria that display a unique division of metabolic labor between cells. Cells in deeper sediment layers are oxidizing sulfide, while cells in the surface layers of the sediment are reducing oxygen. The electrical coupling of these two redox half reactions is ensured via long-distance electron transport through a network of conductive fibers that run in the shared cell envelope of the centimeter-long filament. Here we investigate how this unique electrogenic metabolism is linked to filament growth and cell division. Combining dual-label stable isotope probing (13C and 15N), nanoscale secondary ion mass spectrometry, fluorescence microscopy and genome analysis, we find that the cell cycle of cable bacteria cells is highly comparable to that of other, single-celled Gram-negative bacteria. However, the timing of cell growth and division appears to be tightly and uniquely controlled by long-distance electron transport, as cell division within an individual filament shows a remarkable synchronicity that extends over a millimeter length scale. To explain this, we propose the "oxygen pacemaker" model in which a filament only grows when performing long-distance transport, and the latter is only possible when a filament has access to oxygen so it can discharge electrons from its internal electrical network.
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Affiliation(s)
| | | | | | | | | | | | | | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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Abstract
Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) is an imaging method used to identify microorganisms in environmental samples based on their phylogeny. CARD-FISH can be combined with nano-scale secondary ion mass spectrometry (nanoSIMS) to directly link the cell identity to their activity, measured as the incorporation of stable isotopes into hybridized cells after stable isotope probing. In environmental microbiology, a combination of these methods has been used to determine the identity and growth of uncultured microorganisms, and to explore the factors controlling their activity. Additionally, FISH-nanoSIMS has been widely used to directly visualize microbial interactions in situ. Here, we describe a step-by-step protocol for a combination of CARD-FISH, laser marking, and nanoSIMS analysis on samples from aquatic environments.
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Bandara CD, Schmidt M, Davoudpour Y, Stryhanyuk H, Richnow HH, Musat N. Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context. FRONTIERS IN PLANT SCIENCE 2021; 12:668929. [PMID: 34305970 PMCID: PMC8293618 DOI: 10.3389/fpls.2021.668929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 05/12/2023]
Abstract
During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro- to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.
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Henkel JV, Vogts A, Werner J, Neu TR, Spröer C, Bunk B, Schulz-Vogt HN. Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Syst Appl Microbiol 2020; 44:126155. [PMID: 33278714 DOI: 10.1016/j.syapm.2020.126155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL-1 (optimum 25gL-1). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL-1 (optimum 21gL-1). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H2), sulfide (H2S here taken as the sum of H2S, HS- and S2-), elemental sulfur (S0) and thiosulfate (S2O32-) as electron donors and nitrate (NO3-), oxygen (O2) and particulate manganese oxide (MnO2) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1T as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.
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Affiliation(s)
- Jan V Henkel
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany.
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Johannes Werner
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, 39114 Magdeburg, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Heide N Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
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Meyer NR, Fortney JL, Dekas AE. NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity. Environ Microbiol 2020; 23:81-98. [PMID: 33000528 DOI: 10.1111/1462-2920.15264] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 12/01/2022]
Abstract
The activity of individual microorganisms can be measured within environmental samples by detecting uptake of isotope-labelled substrates using nano-scale secondary ion mass spectrometry (nanoSIMS). Recent studies have demonstrated that sample preparation can decrease 13 C and 15 N enrichment in bacterial cells, resulting in underestimates of activity. Here, we explore this effect with a variety of preparation types, microbial lineages and isotope labels to determine its consistency and therefore potential for correction. Specifically, we investigated the impact of different protocols for fixation, nucleic acid staining and catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) on >14 500 archaeal and bacterial cells (Methanosarcina acetivorans, Sulfolobus acidocaldarius and Pseudomonas putida) enriched in 13 C, 15 N, 18 O, 2 H and/or 34 S. We found these methods decrease isotope enrichments by up to 80% - much more than previously reported - and that the effect varies by taxa, growth phase, isotope label and applied protocol. We make recommendations for how to account for this effect experimentally and analytically. We also re-evaluate published nanoSIMS datasets and revise estimated microbial turnover times in the marine subsurface and nitrogen fixation rates in pelagic unicellular cyanobacteria. When sample preparation is accounted for, cell-specific rates increase and are more consistent with modelled and bulk rates.
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Affiliation(s)
- Nicolette R Meyer
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Julian L Fortney
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
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Prochlorococcus Cells Rely on Microbial Interactions Rather than on Chlorotic Resting Stages To Survive Long-Term Nutrient Starvation. mBio 2020; 11:mBio.01846-20. [PMID: 32788385 PMCID: PMC7439483 DOI: 10.1128/mbio.01846-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ability of microorganisms to withstand long periods of nutrient starvation is key to their survival and success under highly fluctuating conditions that are common in nature. Therefore, one would expect this trait to be prevalent among organisms in the nutrient-poor open ocean. Here, we show that this is not the case for Prochlorococcus, a globally abundant and ecologically important marine cyanobacterium. Instead, Prochlorococcus relies on co-occurring heterotrophic bacteria to survive extended phases of nutrient and light starvation. Our results highlight the power of microbial interactions to drive major biogeochemical cycles in the ocean and elsewhere with consequences at the global scale. Many microorganisms produce resting cells with very low metabolic activity that allow them to survive phases of prolonged nutrient or energy stress. In cyanobacteria and some eukaryotic phytoplankton, the production of resting stages is accompanied by a loss of photosynthetic pigments, a process termed chlorosis. Here, we show that a chlorosis-like process occurs under multiple stress conditions in axenic laboratory cultures of Prochlorococcus, the dominant phytoplankton linage in large regions of the oligotrophic ocean and a global key player in ocean biogeochemical cycles. In Prochlorococcus strain MIT9313, chlorotic cells show reduced metabolic activity, measured as C and N uptake by Nanoscale secondary ion mass spectrometry (NanoSIMS). However, unlike many other cyanobacteria, chlorotic Prochlorococcus cells are not viable and do not regrow under axenic conditions when transferred to new media. Nevertheless, cocultures with a heterotrophic bacterium, Alteromonas macleodii HOT1A3, allowed Prochlorococcus to survive nutrient starvation for months. We propose that reliance on co-occurring heterotrophic bacteria, rather than the ability to survive extended starvation as resting cells, underlies the ecological success of Prochlorococcus.
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Abstract
Manganese is among Earth’s most abundant elements. Its oxidation had long been theorized1, yet undemonstrated2–4, to fuel chemolithoautotrophic microbial growth. Here, an enrichment culture exhibiting Mn(II)-oxidation-dependent, exponential growth was refined to a two species co-culture. Oxidation required viable bacteria at permissive temperatures, resulting in the generation of small Mn oxide nodules to which the cells associated. The majority member of the culture, ‘Candidatus Manganitrophus noduliformans’, affiliates within phylum Nitrospirae (Nitrospirota) but is distantly related to known Nitrospira and Leptospirillum species. The minority member has been isolated, but does not oxidise Mn(II) alone. Stable isotope probing revealed Mn(II)-oxidation-dependent, 13CO2-fixation into cellular biomass. Transcriptomics reveals candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and to autotrophic CO2-fixation. These findings expand the known diversity of inorganic metabolisms supporting life, while completing a biogeochemical energy cycle for manganese5,6, one that may interface with other major global elemental cycles.
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Contat C, Ancey PB, Zangger N, Sabatino S, Pascual J, Escrig S, Jensen L, Goepfert C, Lanz B, Lepore M, Gruetter R, Rossier A, Berezowska S, Neppl C, Zlobec I, Clerc-Rosset S, Knott GW, Rathmell JC, Abel ED, Meibom A, Meylan E. Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth. eLife 2020; 9:e53618. [PMID: 32571479 PMCID: PMC7311173 DOI: 10.7554/elife.53618] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/05/2020] [Indexed: 12/16/2022] Open
Abstract
Glucose utilization increases in tumors, a metabolic process that is observed clinically by 18F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET). However, is increased glucose uptake important for tumor cells, and which transporters are implicated in vivo? In a genetically-engineered mouse model of lung adenocarcinoma, we show that the deletion of only one highly expressed glucose transporter, Glut1 or Glut3, in cancer cells does not impair tumor growth, whereas their combined loss diminishes tumor development. 18F-FDG-PET analyses of tumors demonstrate that Glut1 and Glut3 loss decreases glucose uptake, which is mainly dependent on Glut1. Using 13C-glucose tracing with correlated nanoscale secondary ion mass spectrometry (NanoSIMS) and electron microscopy, we also report the presence of lamellar body-like organelles in tumor cells accumulating glucose-derived biomass, depending partially on Glut1. Our results demonstrate the requirement for two glucose transporters in lung adenocarcinoma, the dual blockade of which could reach therapeutic responses not achieved by individual targeting.
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Affiliation(s)
- Caroline Contat
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
| | - Pierre-Benoit Ancey
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
| | - Nadine Zangger
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
- Bioinformatics Core Facility, Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Silvia Sabatino
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
| | - Justine Pascual
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Louise Jensen
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Christine Goepfert
- Institute of Animal Pathology (COMPATH), University of Bern, CH-3012 Bern, and Histology Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Bernard Lanz
- Laboratory for Functional and Metabolic Imaging (LIFMET), Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Mario Lepore
- Center for Biomedical Imaging (CIBM), Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Rolf Gruetter
- Laboratory for Functional and Metabolic Imaging (LIFMET), Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Center for Biomedical Imaging (CIBM), Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Anouk Rossier
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
| | | | | | - Inti Zlobec
- Institute of Pathology, University of BernBernSwitzerland
| | - Stéphanie Clerc-Rosset
- BioEM Facility, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Graham William Knott
- BioEM Facility, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Jeffrey C Rathmell
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical CenterNashvilleUnited States
| | - E Dale Abel
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Carver College of Medicine, University of IowaIowa CityUnited States
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Center for Advanced Surface Analysis, Faculty of Geosciences and Environment, University of LausanneLausanneSwitzerland
| | - Etienne Meylan
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Cancer Center LémanLausanneSwitzerland
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50
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LeKieffre C, Spero HJ, Fehrenbacher JS, Russell AD, Ren H, Geslin E, Meibom A. Ammonium is the preferred source of nitrogen for planktonic foraminifer and their dinoflagellate symbionts. Proc Biol Sci 2020; 287:20200620. [PMID: 32546098 PMCID: PMC7329048 DOI: 10.1098/rspb.2020.0620] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The symbiotic planktonic foraminifera Orbulina universa inhabits open ocean oligotrophic ecosystems where dissolved nutrients are scarce and often limit biological productivity. It has previously been proposed that O. universa meets its nitrogen (N) requirements by preying on zooplankton, and that its symbiotic dinoflagellates recycle metabolic ‘waste ammonium’ for their N pool. However, these conclusions were derived from bulk 15N-enrichment experiments and model calculations, and our understanding of N assimilation and exchange between the foraminifer host cell and its symbiotic dinoflagellates remains poorly constrained. Here, we present data from pulse-chase experiments with 13C-enriched inorganic carbon, 15N-nitrate, and 15N-ammonium, as well as a 13C- and 15N- enriched heterotrophic food source, followed by TEM (transmission electron microscopy) coupled to NanoSIMS (nanoscale secondary ion mass spectrometry) isotopic imaging to visualize and quantify C and N assimilation and translocation in the symbiotic system. High levels of 15N-labelling were observed in the dinoflagellates and in foraminiferal organelles and cytoplasm after incubation with 15N-ammonium, indicating efficient ammonium assimilation. Only weak 15N-assimilation was observed after incubation with 15N-nitrate. Feeding foraminifers with 13C- and 15N-labelled food resulted in dinoflagellates that were labelled with 15N, thereby confirming the transfer of 15N-compounds from the digestive vacuoles of the foraminifer to the symbiotic dinoflagellates, likely through recycling of ammonium. These observations are important for N isotope-based palaeoceanographic reconstructions, as they show that δ15N values recorded in the organic matrix in symbiotic species likely reflect ammonium recycling rather than alternative N sources, such as nitrates.
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Affiliation(s)
- Charlotte LeKieffre
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland.,UMR CNRS 6112 - LPG-BIAF, Université d'Angers, 49045 Angers Cedex, France
| | - Howard J Spero
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA 95616, USA
| | - Jennifer S Fehrenbacher
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Ann D Russell
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA 95616, USA
| | - Haojia Ren
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Emmanuelle Geslin
- UMR CNRS 6112 - LPG-BIAF, Université d'Angers, 49045 Angers Cedex, France
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Switzerland
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