1
|
Ji R, Wan J, Liu J, Zheng J, Xiao T, Pan Y, Lin W. Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level. MICROBIOME 2024; 12:158. [PMID: 39182147 PMCID: PMC11344931 DOI: 10.1186/s40168-024-01837-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/14/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques. METHODS Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics. RESULTS We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time. CONCLUSIONS To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.
Collapse
Affiliation(s)
- Runjia Ji
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Wan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
| | - Jia Liu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinbo Zheng
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Engineering Laboratory for Deep Resources Equipment and Technology, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Tian Xiao
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
2
|
Awal RP, Müller FD, Pfeiffer D, Monteil CL, Perrière G, Lefèvre CT, Schüler D. Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense. mBio 2023; 14:e0164923. [PMID: 37823629 PMCID: PMC10653835 DOI: 10.1128/mbio.01649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains, which are organized by the actin-like MamK protein. Although MamK is the most highly conserved magnetosome protein common to all MTB, its analysis has been confined to a small subgroup owing to the inaccessibility of most MTB. Our study takes advantage of a genetically tractable host where expression of diverse MamK orthologs together with a resurrected MamK LUCA and uncharacterized actin-like Mad28 proteins from deep-branching MTB resulted in gradual restoration of magnetosome chains in various mutants. Our results further indicate the existence of species-specific MamK interactors and shed light on the evolutionary relationships of one of the key proteins associated with bacterial magnetotaxis.
Collapse
Affiliation(s)
- Ram Prasad Awal
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Frank D. Müller
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Daniel Pfeiffer
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| | - Caroline L. Monteil
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard-Lyon 1, Villeurbanne, France
| | - Christopher T. Lefèvre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Dirk Schüler
- Department of Microbiology, Universitat Bayreuth, Bayreuth, Germany
| |
Collapse
|
3
|
Zhao Y, Zhang W, Pan H, Chen J, Cui K, Wu LF, Lin W, Xiao T, Zhang W, Liu J. Insight into the metabolic potential and ecological function of a novel Magnetotactic Nitrospirota in coral reef habitat. Front Microbiol 2023; 14:1182330. [PMID: 37342564 PMCID: PMC10278575 DOI: 10.3389/fmicb.2023.1182330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/21/2023] [Indexed: 06/23/2023] Open
Abstract
Magnetotactic bacteria (MTB) within the Nitrospirota phylum play important roles in biogeochemical cycles due to their outstanding ability to biomineralize large amounts of magnetite magnetosomes and intracellular sulfur globules. For several decades, Nitrospirota MTB were believed to only live in freshwater or low-salinity environments. While this group have recently been found in marine sediments, their physiological features and ecological roles have remained unclear. In this study, we combine electron microscopy with genomics to characterize a novel population of Nitrospirota MTB in a coral reef area of the South China Sea. Both phylogenetic and genomic analyses revealed it as representative of a novel genus, named as Candidatus Magnetocorallium paracelense XS-1. The cells of XS-1 are small and vibrioid-shaped, and have bundled chains of bullet-shaped magnetite magnetosomes, sulfur globules, and cytoplasmic vacuole-like structures. Genomic analysis revealed that XS-1 has the potential to respire sulfate and nitrate, and utilize the Wood-Ljungdahl pathway for carbon fixation. XS-1 has versatile metabolic traits that make it different from freshwater Nitrospirota MTB, including Pta-ackA pathway, anaerobic sulfite reduction, and thiosulfate disproportionation. XS-1 also encodes both the cbb3-type and the aa3-type cytochrome c oxidases, which may function as respiratory energy-transducing enzymes under high oxygen conditions and anaerobic or microaerophilic conditions, respectively. XS-1 has multiple copies of circadian related genes in response to variability in coral reef habitat. Our results implied that XS-1 has a remarkable plasticity to adapt the environment and can play a beneficial role in coral reef ecosystems.
Collapse
Affiliation(s)
- Yicong Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wenyan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Hongmiao Pan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| | | | - Kaixuan Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Long-Fei Wu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
- Aix Marseille University, CNRS, LCB, IM2B, IMM, Marseille, France
| | - Wei Lin
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Tian Xiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| | - Wuchang Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jia Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Large-Scale Cultivation of Magnetotactic Bacteria and the Optimism for Sustainable and Cheap Approaches in Nanotechnology. Mar Drugs 2023; 21:md21020060. [PMID: 36827100 PMCID: PMC9961000 DOI: 10.3390/md21020060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Magnetotactic bacteria (MTB), a diverse group of marine and freshwater microorganisms, have attracted the scientific community's attention since their discovery. These bacteria biomineralize ferrimagnetic nanocrystals, the magnetosomes, or biological magnetic nanoparticles (BMNs), in a single or multiple chain(s) within the cell. As a result, cells experience an optimized magnetic dipolar moment responsible for a passive alignment along the lines of the geomagnetic field. Advances in MTB cultivation and BMN isolation have contributed to the expansion of the biotechnological potential of MTB in recent decades. Several studies with mass-cultured MTB expanded the possibilities of using purified nanocrystals and whole cells in nano- and biotechnology. Freshwater MTB were primarily investigated in scaling up processes for the production of BMNs. However, marine MTB have the potential to overcome freshwater species applications due to the putative high efficiency of their BMNs in capturing molecules. Regarding the use of MTB or BMNs in different approaches, the application of BMNs in biomedicine remains the focus of most studies, but their application is not restricted to this field. In recent years, environment monitoring and recovery, engineering applications, wastewater treatment, and industrial processes have benefited from MTB-based biotechnologies. This review explores the advances in MTB large-scale cultivation and the consequent development of innovative tools or processes.
Collapse
|
5
|
Goswami P, He K, Li J, Pan Y, Roberts AP, Lin W. Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications. NPJ Biofilms Microbiomes 2022; 8:43. [PMID: 35650214 PMCID: PMC9160268 DOI: 10.1038/s41522-022-00304-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 05/04/2022] [Indexed: 11/08/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a group of phylogenetically diverse and morphologically varied microorganisms with a magnetoresponsive capability called magnetotaxis or microbial magnetoreception. MTB are a distinctive constituent of the microbiome of aquatic ecosystems because they use Earth's magnetic field to align themselves in a north or south facing direction and efficiently navigate to their favored microenvironments. They have been identified worldwide from diverse aquatic and waterlogged microbiomes, including freshwater, saline, brackish and marine ecosystems, and some extreme environments. MTB play important roles in the biogeochemical cycling of iron, sulphur, phosphorus, carbon and nitrogen in nature and have been recognized from in vitro cultures to sequester heavy metals like selenium, cadmium, and tellurium, which makes them prospective candidate organisms for aquatic pollution bioremediation. The role of MTB in environmental systems is not limited to their lifespan; after death, fossil magnetosomal magnetic nanoparticles (known as magnetofossils) are a promising proxy for recording paleoenvironmental change and geomagnetic field history. Here, we summarize the ecology, evolution, and environmental function of MTB and the paleoenvironmental implications of magnetofossils in light of recent discoveries.
Collapse
Affiliation(s)
- Pranami Goswami
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 100029, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, 100029, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- Research School of Earth Sciences, Australian National University, ACT, Canberra, ACT, 2601, Australia
| | - Kuang He
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 100029, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, 100029, Beijing, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Submarine Geosciences and Prospecting Techniques, MoE and College of Marine Geosciences, Ocean University of China, 266100, Qingdao, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 100029, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, 100029, Beijing, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 100029, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, 100029, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, ACT, Canberra, ACT, 2601, Australia.
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 100029, Beijing, China.
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, 100029, Beijing, China.
| |
Collapse
|
6
|
Mao X, Egli R, Liu X, Zhao L. Magnetotactic advantage in stable sediment by long-term observations of magnetotactic bacteria in Earth’s field, zero field and alternating field. PLoS One 2022; 17:e0263593. [PMID: 35202421 PMCID: PMC8870540 DOI: 10.1371/journal.pone.0263593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
Magnetotactic bacteria (MTB) rely on magnetotaxis to effectively reach their preferred living habitats, whereas experimental investigation of magnetotactic advantage in stable sediment is currently lacking. We studied two wild type MTB (cocci and rod-shaped M. bavaricum) in sedimentary environment under exposure to geomagnetic field in the laboratory, zero field and an alternating field whose polarity was switched every 24 hours. The mean concentration of M. bavaricum dropped by ~50% during 6 months in zero field, with no clear temporal trend suggesting an extinction. Cell numbers recovered to initial values within ~1.5 months after the Earth’s field was reset. Cocci displayed a larger temporal variability with no evident population changes in zero field. The alternating field experiment produced a moderate decrease of M. bavaricum concentrations and nearby extinction of cocci, confirming the active role of magnetotaxis in sediment and might point to a different magnetotactic mechanism for M. bavaricum which possibly benefited them to survive field reversals in geological periods. Our findings provide a first quantification of magnetotaxis advantage in sedimentary environment.
Collapse
Affiliation(s)
- Xuegang Mao
- College of Geographical Sciences, Fujian Normal University, Fuzhou, China
- Institute of Geography, Fujian Normal University, Fuzhou, China
- * E-mail:
| | - Ramon Egli
- Central institute for Meteorology and Geodynamics, Vienna, Austria
| | - Xiuming Liu
- College of Geographical Sciences, Fujian Normal University, Fuzhou, China
- Institute of Geography, Fujian Normal University, Fuzhou, China
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Lijuan Zhao
- College of Geographical Sciences, Fujian Normal University, Fuzhou, China
| |
Collapse
|
7
|
Barr CR, Bedrossian M, Lohmann KJ, Nealson KH. Magnetotactic bacteria: concepts, conundrums, and insights from a novel in situ approach using digital holographic microscopy (DHM). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:107-124. [DOI: 10.1007/s00359-022-01543-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 11/25/2022]
|
8
|
Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
Collapse
Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| |
Collapse
|
9
|
Zhang W, Wang Y, Liu L, Pan Y, Lin W. Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae. Front Microbiol 2021; 12:690052. [PMID: 34385986 PMCID: PMC8353452 DOI: 10.3389/fmicb.2021.690052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 11/23/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a group of microbes that biomineralize membrane-bound, nanosized magnetite (Fe3O4), and/or greigite (Fe3S4) crystals in intracellular magnetic organelle magnetosomes. MTB belonging to the Nitrospirae phylum can form up to several hundreds of Fe3O4 magnetosome crystals and dozens of sulfur globules in a single cell. These MTB are widespread in aquatic environments and sometimes account for a significant proportion of microbial biomass near the oxycline, linking these lineages to the key steps of global iron and sulfur cycling. Despite their ecological and biogeochemical importance, our understanding of the diversity and ecophysiology of magnetotactic Nitrospirae is still very limited because this group of MTB remains unculturable. Here, we identify and characterize two previously unknown MTB populations within the Nitrospirae phylum through a combination of 16S rRNA gene-based and genome-resolved metagenomic analyses. These two MTB populations represent distinct morphotypes (rod-shaped and coccoid, designated as XYR, and XYC, respectively), and both form more than 100 bullet-shaped magnetosomal crystals per cell. High-quality draft genomes of XYR and XYC have been reconstructed, and they represent a novel species and a novel genus, respectively, according to their average amino-acid identity values with respect to available genomes. Accordingly, the names Candidatus Magnetobacterium cryptolimnobacter and Candidatus Magnetomicrobium cryptolimnococcus for XYR and XYC, respectively, were proposed. Further comparative genomic analyses of XYR, XYC, and previously reported magnetotactic Nitrospirae reveal the general metabolic potential of this MTB group in distinct microenvironments, including CO2 fixation, dissimilatory sulfate reduction, sulfide oxidation, nitrogen fixation, or denitrification processes. A remarkably conserved magnetosome gene cluster has been identified across Nitrospirae MTB genomes, indicating its putative important adaptive roles in these bacteria. Taken together, the present study provides novel insights into the phylogenomic diversity and ecophysiology of this intriguing, yet poorly understood MTB group.
Collapse
Affiliation(s)
- Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
10
|
Busigny V, Mathon FP, Jézéquel D, Bidaud CC, Viollier E, Bardoux G, Bourrand JJ, Benzerara K, Duprat E, Menguy N, Monteil CL, Lefevre CT. Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France. Environ Microbiol 2021; 24:721-736. [PMID: 33687779 DOI: 10.1111/1462-2920.15458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 01/16/2023]
Abstract
Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.
Collapse
Affiliation(s)
- Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Institut Universitaire de France, Paris, 75005, France
| | - François P Mathon
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, 74200, France
| | - Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Eric Viollier
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Gérard Bardoux
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Jean-Jacques Bourrand
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| |
Collapse
|
11
|
Uzun M, Alekseeva L, Krutkina M, Koziaeva V, Grouzdev D. Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases. Sci Data 2020; 7:252. [PMID: 32737307 PMCID: PMC7449369 DOI: 10.1038/s41597-020-00593-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
Collapse
Affiliation(s)
- Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Lolita Alekseeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Denis Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| |
Collapse
|
12
|
Amor M, Mathon FP, Monteil CL, Busigny V, Lefevre CT. Iron-biomineralizing organelle in magnetotactic bacteria: function, synthesis and preservation in ancient rock samples. Environ Microbiol 2020; 22:3611-3632. [PMID: 32452098 DOI: 10.1111/1462-2920.15098] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 12/22/2022]
Abstract
Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that incorporate iron from their environment to synthesize intracellular nanoparticles of magnetite (Fe3 O4 ) or greigite (Fe3 S4 ) in a genetically controlled manner. Magnetite and greigite magnetic phases allow MTB to swim towards redox transition zones where they thrive. MTB may represent some of the oldest microorganisms capable of synthesizing minerals on Earth and have been proposed to significantly impact the iron biogeochemical cycle by immobilizing soluble iron into crystals that subsequently fossilize in sedimentary rocks. In the present article, we describe the distribution of MTB in the environment and discuss the possible function of the magnetite and greigite nanoparticles. We then provide an overview of the chemical mechanisms leading to iron mineralization in MTB. Finally, we update the methods used for the detection of MTB crystals in sedimentary rocks and present their occurrences in the geological record.
Collapse
Affiliation(s)
- Matthieu Amor
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - François P Mathon
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France.,Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris, F-75005, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Vincent Busigny
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris, F-75005, France.,Institut Universitaire de France, Paris, 75005, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| |
Collapse
|
13
|
Geesink P, Wegner CE, Probst AJ, Herrmann M, Dam HT, Kaster AK, Küsel K. Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater. Environ Microbiol 2019; 22:726-737. [PMID: 31742865 DOI: 10.1111/1462-2920.14865] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.
Collapse
Affiliation(s)
- Patricia Geesink
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Alexander J Probst
- Department for Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martina Herrmann
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Hang T Dam
- Institute for Biological Interfaces (IGB 5), Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany.,DSMZ, Braunschweig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IGB 5), Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany.,DSMZ, Braunschweig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
14
|
Qian XX, Liu J, Menguy N, Li J, Alberto F, Teng Z, Xiao T, Zhang W, Wu LF. Identification of novel species of marine magnetotactic bacteria affiliated with Nitrospirae phylum. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:330-337. [PMID: 30980502 DOI: 10.1111/1758-2229.12755] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Magnetotactic bacteria (MTB) are a group of Gram-negative bacteria characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Phylogenetically, they belong to different taxonomic lineages including Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes phyla on the phylogenetic tree. To date, six Nitrospirae MTB phylotypes have been identified from freshwater or low-salinity environments and described in the literature. Here, we report the identification of two Nitrospirae MTB phylotypes collected, for the first time, from the marine environment. Both have a spherical morphology with a cell size of ~ 5 μM and similar motility but are different colours (black-brown and ivory-white) under the optic microscope. They synthesized bullet-shaped iron-oxide magnetosomes that were arranged in multiple bundles of chains. Moreover, the cytoplasm of the black-brown Nitrospirae MTB contained sulphur inclusions that conferred on cells a rough, granular appearance. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they are two novel species and cluster with the previously reported MTB affiliated with the phylum Nitrospirae, thus extending the distribution of Nitrospirae MTB from freshwater to the marine environment.
Collapse
Affiliation(s)
- Xin-Xin Qian
- Aix Marseille University, CNRS, LCB, Marseille, 13402, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
| | - Jia Liu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Nicolas Menguy
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS-Sorbonne Université, F-75005, Paris, France
| | - Jinhua Li
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
| | - François Alberto
- Aix Marseille University, CNRS, LCB, Marseille, 13402, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
| | - Zhaojie Teng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Tian Xiao
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Wenyan Zhang
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Long-Fei Wu
- Aix Marseille University, CNRS, LCB, Marseille, 13402, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille, 13402, France
| |
Collapse
|
15
|
Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. Nat Microbiol 2019; 4:1088-1095. [PMID: 31036911 DOI: 10.1038/s41564-019-0432-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/18/2019] [Indexed: 12/31/2022]
Abstract
Mutualistic symbioses are often a source of evolutionary innovation and drivers of biological diversification1. Widely distributed in the microbial world, particularly in anoxic settings2,3, they often rely on metabolic exchanges and syntrophy2,4. Here, we report a mutualistic symbiosis observed in marine anoxic sediments between excavate protists (Symbiontida, Euglenozoa)5 and ectosymbiotic Deltaproteobacteria biomineralizing ferrimagnetic nanoparticles. Light and electron microscopy observations as well as genomic data support a multi-layered mutualism based on collective magnetotactic motility with division of labour and interspecies hydrogen-transfer-based syntrophy6. The guided motility of the consortia along the geomagnetic field is allowed by the magnetic moment of the non-motile ectosymbiotic bacteria combined with the protist motor activity, which is a unique example of eukaryotic magnetoreception7 acquired by symbiosis. The nearly complete deltaproteobacterial genome assembled from a single consortium contains a full magnetosome gene set8, but shows signs of reduction, with the probable loss of flagellar genes. Based on the metabolic gene content, the ectosymbiotic bacteria are anaerobic sulfate-reducing chemolithoautotrophs that likely reduce sulfate with hydrogen produced by hydrogenosome-like organelles6 underlying the plasma membrane of the protist. In addition to being necessary hydrogen sinks, ectosymbionts may provide organics to the protist by diffusion and predation, as shown by magnetosome-containing digestive vacuoles. Phylogenetic analyses of 16S and 18S ribosomal RNA genes from magnetotactic consortia in marine sediments across the Northern and Southern hemispheres indicate a host-ectosymbiont specificity and co-evolution. This suggests a historical acquisition of magnetoreception by a euglenozoan ancestor from Deltaproteobacteria followed by subsequent diversification. It also supports the cosmopolitan nature of this type of symbiosis in marine anoxic sediments.
Collapse
|
16
|
Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park. Appl Environ Microbiol 2018; 84:AEM.02894-17. [PMID: 29602784 DOI: 10.1128/aem.02894-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and 13C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter, Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.
Collapse
|
17
|
Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y. Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution. ISME JOURNAL 2018; 12:1508-1519. [PMID: 29581530 PMCID: PMC5955933 DOI: 10.1038/s41396-018-0098-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022]
Abstract
The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and "Candidatus Lambdaproteobacteria" classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.
Collapse
Affiliation(s)
- Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Greig A Paterson
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZE, UK
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China. .,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
18
|
Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium". Appl Environ Microbiol 2018; 84:AEM.02224-17. [PMID: 29247059 PMCID: PMC5812927 DOI: 10.1128/aem.02224-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 12/08/2017] [Indexed: 01/16/2023] Open
Abstract
Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4·2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name “Candidatus Sulfobium mesophilum,” gen. nov., sp. nov. IMPORTANCE Rice paddies are indispensable for the food supply but are a major source of the greenhouse gas methane. If it were not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach with Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylum Nitrospirae. This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed it in anoxic paddy soil under sulfate-enriched conditions. Phylogenomics and comparison to the results of environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent an undiscovered genus within the little-explored phylum Nitrospirae. Our results will be important for the design of enrichment strategies and postgenomic studies to further understanding of the contribution of these novel Nitrospirae spp. to the global sulfur cycle.
Collapse
|
19
|
He K, Gilder SA, Orsi WD, Zhao X, Petersen N. Constant Flux of Spatial Niche Partitioning through High-Resolution Sampling of Magnetotactic Bacteria. Appl Environ Microbiol 2017; 83:e01382-17. [PMID: 28778897 PMCID: PMC5626982 DOI: 10.1128/aem.01382-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria (MTB) swim along magnetic field lines in water. They are found in aquatic habitats throughout the world, yet knowledge of their spatial and temporal distribution remains limited. To help remedy this, we took MTB-bearing sediment from a natural pond, mixed the thoroughly homogenized sediment into two replicate aquaria, and then counted three dominant MTB morphotypes (coccus, spirillum, and rod-shaped MTB cells) at a high spatiotemporal sampling resolution: 36 discrete points in replicate aquaria were sampled every ∼30 days over 198 days. Population centers of the MTB coccus and MTB spirillum morphotypes moved in continual flux, yet they consistently inhabited separate locations, displaying significant anticorrelation. Rod-shaped MTB were initially concentrated toward the northern end of the aquaria, but at the end of the experiment, they were most densely populated toward the south. The finding that the total number of MTB cells increased over time during the experiment argues that population reorganization arose from relative changes in cell division and death and not from migration. The maximum net growth rates were 10, 3, and 1 doublings day-1 and average net growth rates were 0.24, 0.11, and 0.02 doublings day-1 for MTB cocci, MTB spirilla, and rod-shaped MTB, respectively; minimum growth rates for all three morphotypes were -0.03 doublings day-1 Our results suggest that MTB cocci and MTB spirilla occupy distinctly different niches: their horizontal positioning in sediment is anticorrelated and under constant flux.IMPORTANCE Little is known about the horizontal distribution of magnetotactic bacteria in sediment or how the distribution changes over time. We therefore measured three dominant magnetotactic bacterium morphotypes at 36 places in two replicate aquaria each month for 7 months. We found that the spatial positioning of population centers changed over time and that the two most abundant morphotypes (MTB cocci and MTB spirilla) occupied distinctly different niches in the aquaria. Maximum and average growth and death rates were quantified for each of the three morphotypes based on 72 sites that were measured six times. The findings provided novel insight into the differential behavior of noncultured magnetotactic bacteria.
Collapse
Affiliation(s)
- Kuang He
- Department of Earth and Environmental Sciences, Ludwig-Maximilians Universität, Munich, Germany
| | - Stuart A Gilder
- Department of Earth and Environmental Sciences, Ludwig-Maximilians Universität, Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians Universität, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians Universität, Munich, Germany
| | - Xiangyu Zhao
- National Institute of Polar Research, Tokyo, Japan
| | - Nikolai Petersen
- Department of Earth and Environmental Sciences, Ludwig-Maximilians Universität, Munich, Germany
| |
Collapse
|
20
|
Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF. The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of P
roteobacteria. Environ Microbiol 2017; 19:1103-1119. [DOI: 10.1111/1462-2920.13637] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Boyang Ji
- Aix Marseille Univ, CNRS, LCB; Marseille France
| | - Sheng-Da Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Wei-Jia Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Zoe Rouy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | - François Alberto
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Claire-Lise Santini
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | | | - Nathalie Pradel
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- Aix Marseille Univ, Univ Toulon, CNRS, IRD; Marseille France
| | | | | | - Ying Li
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Claudine Médigue
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | | | | | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| |
Collapse
|
21
|
Pradel N, Cayol JL, Fardeau ML, Karray F, Sayadi S, Alazard D, Ollivier B. Analysis of a population of magnetotactic bacteria of the Gulf of Gabès, Tunisia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4046-4053. [PMID: 25772882 DOI: 10.1007/s11356-015-4314-0] [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: 12/15/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
The occurrence of magnetotactic bacteria (MTB) on a Tunisian marine coast exposed to heavy metals pollution (Sfax, Gulf of Gabès, Mediterranean Sea) was investigated. The MTB population of this Southern Mediterranean coast was compared to the MTB populations previously investigated on the French Northern Mediterranean coast. A dominant MTB coccus morphotype was observed by microscopy analysis. By pyrosequencing technology, the analysis of the 16S ribosomal RNA (rDNA) revealed as much as 33 operational taxonomic sequence units (OTUs) close to sequences of MTB accessible in the databases. The majority were close to MTB sequences of the "Med group" of α-Proteobacteria. Among them, a dominant OTU_001 (99 % of the MTB sequences) affiliated within the Magnetococcales order was highlighted. Investigating the capacities of this novel bacterium to be used in bioremediation and/or depollution processes could be envisaged.
Collapse
Affiliation(s)
- Nathalie Pradel
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288, Marseille, France.
- Laboratoire Mixte International Contaminants et Ecosystèmes Marins Sud Méditerranéens (LMI COSYS-Med), Marseille, France.
| | - Jean-Luc Cayol
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288, Marseille, France
| | - Marie-Laure Fardeau
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288, Marseille, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Biotechnology Center of Sfax, Sfax, 3018, Tunisia
- Laboratoire Mixte International Contaminants et Ecosystèmes Marins Sud Méditerranéens (LMI COSYS-Med), Marseille, France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, Biotechnology Center of Sfax, Sfax, 3018, Tunisia
- Laboratoire Mixte International Contaminants et Ecosystèmes Marins Sud Méditerranéens (LMI COSYS-Med), Marseille, France
| | - Didier Alazard
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288, Marseille, France
- Laboratoire Mixte International Contaminants et Ecosystèmes Marins Sud Méditerranéens (LMI COSYS-Med), Marseille, France
| |
Collapse
|
22
|
Zhao X, Egli R, Gilder SA, Müller S. Microbially assisted recording of the Earth's magnetic field in sediment. Nat Commun 2016; 7:10673. [PMID: 26864428 PMCID: PMC4753249 DOI: 10.1038/ncomms10673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/08/2016] [Indexed: 11/29/2022] Open
Abstract
Sediments continuously record variations of the Earth's magnetic field and thus provide an important archive for studying the geodynamo. The recording process occurs as magnetic grains partially align with the geomagnetic field during and after sediment deposition, generating a depositional remanent magnetization (DRM) or post-DRM (PDRM). (P)DRM acquisition mechanisms have been investigated for over 50 years, yet many aspects remain unclear. A key issue concerns the controversial role of bioturbation, that is, the mechanical disturbance of sediment by benthic organisms, during PDRM acquisition. A recent theory on bioturbation-driven PDRM appears to solve many inconsistencies between laboratory experiments and palaeomagnetic records, yet it lacks experimental proof. Here we fill this gap by documenting the important role of bioturbation-induced rotational diffusion for (P)DRM acquisition, including the control exerted on the recorded inclination and intensity, as determined by the equilibrium between aligning and perturbing torques acting on magnetic particles. Sediments record variations of the Earth's magnetic field via the alignment of magnetic grains during and after deposition, yet the role of post-depositional processes remains unclear. Here, the authors present experiments showing how microbially-induced bioturbation controls the alignment process.
Collapse
Affiliation(s)
- Xiangyu Zhao
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University, Munich 80333, Germany
| | - Ramon Egli
- Central Institute of Meteorology and Geodynamics (ZAMG), Division Data, Methods and Models, Vienna 1190, Austria
| | - Stuart A Gilder
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University, Munich 80333, Germany
| | - Sebastian Müller
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University, Munich 80333, Germany
| |
Collapse
|
23
|
Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D. Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes. Environ Microbiol 2015; 18:21-37. [PMID: 26060021 DOI: 10.1111/1462-2920.12907] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022]
Abstract
While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus 'Candidatus Magnetobacterium' homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep-branching MTB. Here we report the analysis of single-cell derived draft genomes of three deep-branching uncultivated MTB. Single-cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS-04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK-01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet-shaped magnetosomes and their arrangement in multiple bundles of chains.
Collapse
Affiliation(s)
- Sebastian Kolinko
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Michael Richter
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Frank-Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany.,Department of Life Sciences & Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Andreas Brachmann
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Dirk Schüler
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany.,Department of Microbiology, University Bayreuth, Bayreuth, Germany
| |
Collapse
|
24
|
Kato S, Ikehata K, Shibuya T, Urabe T, Ohkuma M, Yamagishi A. Potential for biogeochemical cycling of sulfur, iron and carbon within massive sulfide deposits below the seafloor. Environ Microbiol 2014; 17:1817-35. [DOI: 10.1111/1462-2920.12648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 08/13/2014] [Accepted: 09/25/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Shingo Kato
- Department of Molecular Biology; Tokyo University of Pharmacy and Life Science; 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
- Japan Collection of Microorganisms; RIKEN BioResource Center; 3-1-1 Koyadai Tsukuba Ibaraki 305-0074 Japan
| | - Kei Ikehata
- Faculty of Life and Environmental Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Takazo Shibuya
- Submarine Resources Research Project (SRRP) & Precambrian Ecosystem Laboratory (PEL); Japan Agency for Marine-Earth Science and Technology (JAMSTEC); 2-15 Natsushima Yokosuka Kanagawa 237-0061 Japan
| | - Tetsuro Urabe
- Department of Earth and Planetary Science; University of Tokyo; Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms; RIKEN BioResource Center; 3-1-1 Koyadai Tsukuba Ibaraki 305-0074 Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology; Tokyo University of Pharmacy and Life Science; 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| |
Collapse
|
25
|
Eder SHK, Gigler AM, Hanzlik M, Winklhofer M. Sub-micrometer-scale mapping of magnetite crystals and sulfur globules in magnetotactic bacteria using confocal Raman micro-spectrometry. PLoS One 2014; 9:e107356. [PMID: 25233081 PMCID: PMC4169400 DOI: 10.1371/journal.pone.0107356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
The ferrimagnetic mineral magnetite Fe3O4 is biomineralized by magnetotactic microorganisms and a diverse range of animals. Here we demonstrate that confocal Raman microscopy can be used to visualize chains of magnetite crystals in magnetotactic bacteria, even though magnetite is a poor Raman scatterer and in bacteria occurs in typical grain sizes of only 35-120 nm, well below the diffraction-limited optical resolution. When using long integration times together with low laser power (<0.25 mW) to prevent laser induced damage of magnetite, we can identify and map magnetite by its characteristic Raman spectrum (303, 535, 665 cm(-1)) against a large autofluorescence background in our natural magnetotactic bacteria samples. While greigite (cubic Fe3S4; Raman lines of 253 and 351 cm(-1)) is often found in the Deltaproteobacteria class, it is not present in our samples. In intracellular sulfur globules of Candidatus Magnetobacterium bavaricum (Nitrospirae), we identified the sole presence of cyclo-octasulfur (S8: 151, 219, 467 cm(-1)), using green (532 nm), red (638 nm) and near-infrared excitation (785 nm). The Raman-spectra of phosphorous-rich intracellular accumulations point to orthophosphate in magnetic vibrios and to polyphosphate in magnetic cocci. Under green excitation, the cell envelopes are dominated by the resonant Raman lines of the heme cofactor of the b or c-type cytochrome, which can be used as a strong marker for label-free live-cell imaging of bacterial cytoplasmic membranes, as well as an indicator for the redox state.
Collapse
Affiliation(s)
- Stephan H. K. Eder
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander M. Gigler
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-University Munich, Munich, Germany
- Center for NanoScience (CeNS), Munich, Germany
| | - Marianne Hanzlik
- Department of Chemistry, Elektronenmikroskopie, Technical University Munich, Munich, Germany
| | - Michael Winklhofer
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-University Munich, Munich, Germany
- * E-mail:
| |
Collapse
|
26
|
Abstract
Magnetotactic bacteria (MTB) use passive alignment with the Earth magnetic field as a mean to increase their navigation efficiency in horizontally stratified environments through what is known as magneto-aerotaxis (M-A). Current M-A models have been derived from MTB observations in aqueous environments, where a >80% alignment with inclined magnetic field lines produces a one-dimensional search for optimal living conditions. However, the mean magnetic alignment of MTB in their most widespread living environment, i.e. sediment, has been recently found to be <1%, greatly reducing or even eliminating the magnetotactic advantage deduced for the case of MTB in water. In order to understand the role of magnetotaxis for MTB populations living in sediment, we performed first M-A observations with lake sediment microcosms. Microcosm experiments were based on different combinations of (1) MTB position with respect to their preferred living depth (i.e. above, at, and below), and (2) magnetic field configurations (i.e. correctly and incorrectly polarized vertical fields, horizontal fields, and zero fields). Results suggest that polar magnetotaxis is more complex than implied by previous experiments, and revealed unexpected differences between two types of MTB living in the same sediment. Our main findings are: (1) all investigated MTB benefit of a clear magnetotactic advantage when they need to migrate over macroscopic distances for reaching their optimal living depth, (2) magnetotaxis is not used by all MTB under stationary, undisturbed conditions, (3) some MTB can rely only on chemotaxis for macroscopic vertical displacements in sediment while other cannot, and (4) some MTB use a fixed polar M-A mechanisms, while other can switch their M-A polarity, performing what can be considered as a mixed polar-axial M-A. These observations demonstrate that sedimentary M-A is controlled by complex mechanical, chemical, and temporal factors that are poorly reproduced in aqueous environments.
Collapse
|
27
|
Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae. ISME JOURNAL 2014; 8:2463-77. [PMID: 24914800 DOI: 10.1038/ismej.2014.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/27/2014] [Accepted: 05/08/2014] [Indexed: 11/09/2022]
Abstract
Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.
Collapse
|
28
|
Abstract
Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.
Collapse
|
29
|
Moisescu C, Ardelean II, Benning LG. The effect and role of environmental conditions on magnetosome synthesis. Front Microbiol 2014; 5:49. [PMID: 24575087 PMCID: PMC3920197 DOI: 10.3389/fmicb.2014.00049] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/23/2014] [Indexed: 12/14/2022] Open
Abstract
Magnetotactic bacteria (MTB) are considered the model species for the controlled biomineralization of magnetic Fe oxide (magnetite, Fe3O4) or Fe sulfide (greigite, Fe3S4) nanocrystals in living organisms. In MTB, magnetic minerals form as membrane-bound, single-magnetic domain crystals known as magnetosomes and the synthesis of magnetosomes by MTB is a highly controlled process at the genetic level. Magnetosome crystals reveal highest purity and highest quality magnetic properties and are therefore increasingly sought after as novel nanoparticulate biomaterials for industrial and medical applications. In addition, "magnetofossils," have been used as both past terrestrial and potential Martian life biosignature. However, until recently, the general belief was that the morphology of mature magnetite crystals formed by MTB was largely unaffected by environmental conditions. Here we review a series of studies that showed how changes in environmental factors such as temperature, pH, external Fe concentration, external magnetic fields, static or dynamic fluid conditions, and nutrient availability or concentrations can all affect the biomineralization of magnetite magnetosomes in MTB. The resulting variations in magnetic nanocrystals characteristics can have consequence both for their commercial value but also for their use as indicators for ancient life. In this paper we will review the recent findings regarding the influence of variable chemical and physical environmental control factors on the synthesis of magnetosome by MTB, and address the role of MTB in the global biogeochemical cycling of iron.
Collapse
Affiliation(s)
- Cristina Moisescu
- Department of Microbiology, Institute of Biology BucharestBucharest, Romania
| | - Ioan I. Ardelean
- Department of Microbiology, Institute of Biology BucharestBucharest, Romania
| | | |
Collapse
|
30
|
Kostanjšek R, Pašić L, Daims H, Sket B. Structure and community composition of sprout-like bacterial aggregates in a Dinaric Karst subterranean stream. MICROBIAL ECOLOGY 2013; 66:5-18. [PMID: 23314097 DOI: 10.1007/s00248-012-0172-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/25/2012] [Indexed: 06/01/2023]
Abstract
The Vjetrenica cave in the Dinaric Karst hosts a worldwide extraordinarily high cave biodiversity. Beside a diverse and specialized cave fauna, sprout-like formations attached to the bed of the cave stream were observed and described, but not further characterized, almost a century ago. Here we investigated these sprout-like microbial aggregates by the rRNA approach and detailed microscopy. Based on fluorescence in situ hybridization and ultrastructural analysis, the sprout-like formations are morphologically highly organized, and their core consists of a member of a novel deep-branching lineage in the bacterial phylum Nitrospirae. This organism displays an interesting cellular ultrastructure with different kinds of cytoplasmic inclusions and is embedded in a thick extracellular matrix, which contributes to the stability and shape of the aggregates. This novel bacterium has been provisionally classified as "Candidatus Troglogloea absoloni." The surface of the sprout-like aggregates is more diverse than the core. It is colonized by a bacterial biofilm consisting primarily of filamentous Betaproteobacteria, whereas other microbial populations present in the crust include members of the Bacteriodetes, Gammaproteobacteria, Actinombacteria, Alphaproteobacteria, and Planctomycetes, which are intermingled with mineral inclusions. This study represents the first thorough molecular and ultrastructural characterization of the elusive sprout-like bacterial aggregates, which are also found in other cave systems of the Dinaric Karst. The discovery of Ca. Troglogloea absoloni contributes to the known biodiversity of subterranean ecosystems and especially of macroscopic structures formed in caves by microorganisms, whose composition and ecological function often remain enigmatic.
Collapse
Affiliation(s)
- Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| | | | | | | |
Collapse
|
31
|
Yan L, Zhang S, Chen P, Wang W, Wang Y, Li H. Magnetic properties of Acidithiobacillus ferrooxidans. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2013; 33:4026-31. [PMID: 23910310 DOI: 10.1016/j.msec.2013.05.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/01/2013] [Accepted: 05/21/2013] [Indexed: 11/29/2022]
Abstract
Understanding the magnetic properties of magnetotactic bacteria (MTBs) is of great interest in fields of life sciences, geosciences, biomineralization, biomagnetism, and planetary sciences. Acidithiobacillus ferrooxidans (At. ferrooxidans), obtaining energy through the oxidation of ferrous iron and various reduced inorganic sulfur compounds, can synthesize intracellular magnetite magnetosomes. However, the magnetic properties of such microorganism remain unknown. Here we used transmission electronmicroscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD) assay, vibrating sample magnetometer (VSM), magneto-thermogravimetric analysis (MTGA), and low temperature magnetometry to comprehensively investigate the magnetic characteristics of At. ferrooxidans. Results revealed that each cell contained only 1 to 3 magnetite magnetosomes, which were arranged irregularly. The magnetosomes were generally in a stable single-domain (SD) state, but superparamagnetic (SP) magnetite particles were also found. The calcined bacteria exhibited a ferromagnetic behavior with a Curie Temperature of 454 °C and a coercivity of 16.36 mT. Additionally, the low delta ratio (δFC/δZFC=1.27) indicated that there were no intact magnetosome chains in At. ferrooxidans. Our results provided the new insights on the biomineralization of bacterial magnetosomes and magnetic properties of At. ferrooxidans.
Collapse
Affiliation(s)
- Lei Yan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
| | | | | | | | | | | |
Collapse
|
32
|
Lefèvre CT, Trubitsyn D, Abreu F, Kolinko S, de Almeida LGP, de Vasconcelos ATR, Lins U, Schüler D, Ginet N, Pignol D, Bazylinski DA. Monophyletic origin of magnetotaxis and the first magnetosomes. Environ Microbiol 2013; 15:2267-74. [PMID: 23438345 DOI: 10.1111/1462-2920.12097] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 01/14/2013] [Indexed: 11/26/2022]
Abstract
Horizontal gene transfer (HGT), the transfer of genetic material other than by descent, is thought to have played significant roles in the evolution and distribution of genes in prokaryotes. These include those responsible for the ability of motile, aquatic magnetotactic bacteria (MTB) to align and swim along magnetic field lines and the biomineralization of magnetosomes that are responsible for this behaviour. There is some genomic evidence that HGT might be responsible for the distribution of magnetosome genes in different phylogenetic groups of bacteria. For example, in the genomes of a number of MTB, magnetosome genes are present as clusters within a larger structure known as the magnetosome genomic island surrounded by mobile elements such as insertion sequences and transposases as well as tRNA genes. Despite this, there is no strong direct proof of HGT between these organisms. Here we show that a phylogenetic tree based on magnetosome protein amino acid sequences from a number of MTB was congruent with the tree based on the organisms' 16S rRNA gene sequences. This shows that evolution and divergence of these proteins and the 16S rRNA gene occurred similarly. This suggests that magnetotaxis originated monophyletically in the Proteobacteria phylum and implies that the common ancestor of all Proteobacteria was magnetotactic.
Collapse
Affiliation(s)
- Christopher T Lefèvre
- CEA Cadarache/CNRS/Aix-Marseille Université, UMR7265 Service de Biologie Végétale et de Microbiologie Environnementale, Laboratoire de Bioénergétique Cellulaire, 13108, Saint Paul lez Durance, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
High diversity of magnetotactic deltaproteobacteria in a freshwater niche. Appl Environ Microbiol 2013; 79:2813-7. [PMID: 23377941 DOI: 10.1128/aem.03635-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the diversity of magnetotactic bacteria in natural environments is crucial for understanding their contribution to various biological and geological processes. Here we report a high diversity of magnetotactic bacteria in a freshwater site. Ten out of 18 operational taxonomic units (OTUs) were affiliated with the Deltaproteobacteria. Some rod-shaped bacteria simultaneously synthesized greigite and magnetite magnetosomes.
Collapse
|
34
|
Kolinko S, Wanner G, Katzmann E, Kiemer F, Fuchs BM, Schüler D. Clone libraries and single cell genome amplification reveal extended diversity of uncultivated magnetotactic bacteria from marine and freshwater environments. Environ Microbiol 2012; 15:1290-301. [PMID: 23106823 DOI: 10.1111/1462-2920.12004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/07/2012] [Accepted: 09/21/2012] [Indexed: 11/30/2022]
Abstract
Magnetotactic bacteria (MTB), which orient along the earth's magnetic field using magnetosomes, are ubiquitous and abundant in marine and freshwater environments. Previous phylogenetic analysis of diverse MTB has been limited to few cultured species and the most abundant and conspicuous members of natural populations, which were assigned to various lineages of the Proteobacteria, the Nitrospirae phylum as well as the candidate division OP3. However, their known phylogenetic diversity still not matches the large morphological and ultrastructural variability of uncultured MTB found in environmental communities. Here, we used analysis of 16S rRNA gene clone libraries in combination with microsorting and whole-genome amplification to systematically address the entire diversity of uncultured MTB from two different habitats. This approach revealed extensive and novel diversity of MTB within the freshwater and marine sediment samples. In total, single-cell analysis identified eight different phylotypes, which were only partly represented in the clone libraries, and which could be unambiguously assigned to their respective morphotypes. Identified MTB belonged to the Alphaproteobacteria (seven species) and the Nitrospirae phylum (two species). End-sequencing of a small insert library created from WGA-derived DNA of a novel conspicuous magnetotactic vibrio identified genes with highest similarity to two cultivated MTB as well as to other phylogenetic groups. In conclusion, the combination of metagenomic cloning and single cell sorting represents a powerful approach to recover maximum bacterial diversity including low-abundant magnetotactic phylotypes from environmental samples and also provides access to genomic analysis of uncultivated MTB.
Collapse
Affiliation(s)
- Sebastian Kolinko
- Biozentrum der Ludwigs-Maximilians-Universität, Grosshaderner Strasse 2-4, 82 152, Planegg-Martinsried, Germany
| | | | | | | | | | | |
Collapse
|
35
|
Lin W, Wang Y, Pan Y. Short-term effects of temperature on the abundance and diversity of magnetotactic cocci. Microbiologyopen 2012; 1:53-63. [PMID: 22950012 PMCID: PMC3426400 DOI: 10.1002/mbo3.7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 12/06/2011] [Accepted: 12/11/2011] [Indexed: 02/01/2023] Open
Abstract
Temperature is one of the most important climate factors that can regulate the activity and growth of organisms. However, it is so far unclear how temperature influences the abundance and community composition of magnetotactic bacteria (MTB) that mineralize intracellular magnetite and/or greigite magnetosomes and play significant roles in the global iron cycling and sediment magnetization. To address this specific problem, in this study we have assessed the impact of temperature on freshwater magnetotactic cocci through laboratory microcosm simulations. Microcosms containing MTB were exposed to four constant temperatures ranging from 9°C to 37°C. After 10 days and 28 days of incubation, no significant differences in abundance were detected in microcosms at 9°C, 15°C, and 26°C (Student's t-test, P > 0.05); however, microcosms exposed to 37°C exhibited a significant decrease of magnetotactic cocci abundance (P < 0.05). Dendrogram analysis of community-amplified ribosomal DNA restriction analysis (community ARDRA) banding patterns distinguished the 37°C samples from samples at lower temperatures regardless of incubation periods. Furthermore, clone library analysis revealed that most of the operational taxonomic units (OTUs) detected in samples from 9°C to 26°C were absent from the 37°C microcosms, whereas six OTUs were exclusively detected in the 37°C samples. Community compositions from four incubation temperatures were further compared using statistical phylogenetic methods (UniFrac and LIBSHUFF), which revealed that the 37°C samples harbored phylogenetically distinct MTB communities compared to those found in 9°C, 15°C, and 26°C samples. Taken together, our results indicate that elevated temperature can influence the abundance and diversity of dominant members of magnetotactic cocci. This linkage further infers that the abundance and diversity of MTB (e.g., based on the fossil magnetosomes) may be useful in reconstruction of paleotemperature.
Collapse
Affiliation(s)
- Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
- France-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
| | - Yinzhao Wang
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
- France-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
- France-China Bio-Mineralization and Nano-Structures Laboratory, Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029, China
| |
Collapse
|
36
|
Zeytuni N, Baran D, Davidov G, Zarivach R. Inter-phylum structural conservation of the magnetosome-associated TPR-containing protein, MamA. J Struct Biol 2012; 180:479-87. [PMID: 22917855 DOI: 10.1016/j.jsb.2012.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
Abstract
Magnetotactic bacteria enclose the magnetosome, a unique prokaryotic sub-cellular organelle that allows the biomineralization of magnetic nano-crystals. Membrane-coated magnetosomes are arranged into a linear chain that permits magnetotactic bacteria to navigate geomagnetic fields. Magnetosome assembly and biomineralization are controlled by conserved magnetosome-associated proteins, including MamA, a tetra-trico-peptide repeat (TPR)-containing protein that was shown to coat the magnetosome membrane. In this study, two MamA structures from Candidatus Magnetobacterium bavaricum (Mbav) were determined via X-ray crystallography. These structures confirm that Mbav MamA folds as a sequential TPR protein and shares a high degree of structural similarity with homologous MamA proteins from Magnetospirillum species. Furthermore, the two TPR-containing domains of MamA are separated by an interphylum-conserved region containing a flexible hinge that is involved in ligand binding and recognition. Finally, substantial differences were found in the local stabilization of the MamA N-terminal domain as a result of the loss of an evolutionary conserved salt bridge.
Collapse
Affiliation(s)
- Natalie Zeytuni
- Department of Life Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | | | | | | |
Collapse
|
37
|
Handley KM, Wrighton KC, Piceno YM, Andersen GL, DeSantis TZ, Williams KH, Wilkins MJ, N'Guessan AL, Peacock A, Bargar J, Long PE, Banfield JF. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiol Ecol 2012; 81:188-204. [PMID: 22432531 DOI: 10.1111/j.1574-6941.2012.01363.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 02/27/2012] [Accepted: 03/09/2012] [Indexed: 11/29/2022] Open
Abstract
There is increasing interest in harnessing the functional capacities of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Information about which community members respond to stimulation can guide the interpretation and development of remediation approaches. To comprehensively determine community membership and abundance patterns among a suite of samples associated with uranium bioremediation experiments, we employed a high-density microarray (PhyloChip). Samples were unstimulated, naturally reducing, or collected during Fe(III) (early) and sulfate reduction (late biostimulation) from an acetate re-amended/amended aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Deep community sampling with PhyloChip identified hundreds-to-thousands of operational taxonomic units (OTUs) present during amendment, and revealed close similarity among highly enriched taxa from drill core and groundwater well-deployed column sediment. Overall, phylogenetic data suggested that stimulated community membership was most affected by a carryover effect between annual stimulation events. Nevertheless, OTUs within the Fe(III)- and sulfate-reducing lineages, Desulfuromonadales and Desulfobacterales, were repeatedly stimulated. Less consistent, co-enriched taxa represented additional lineages associated with Fe(III) and sulfate reduction (e.g. Desulfovibrionales; Syntrophobacterales; Peptococcaceae) and autotrophic sulfur oxidation (Sulfurovum; Campylobacterales). Data implies complex membership among highly stimulated taxa and, by inference, biogeochemical responses to acetate, a nonfermentable substrate.
Collapse
Affiliation(s)
- Kim M Handley
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Komeili A. Molecular mechanisms of compartmentalization and biomineralization in magnetotactic bacteria. FEMS Microbiol Rev 2012; 36:232-55. [PMID: 22092030 DOI: 10.1111/j.1574-6976.2011.00315.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Magnetotactic bacteria (MB) are remarkable organisms with the ability to exploit the earth's magnetic field for navigational purposes. To do this, they build specialized compartments called magnetosomes that consist of a lipid membrane and a crystalline magnetic mineral. These organisms have the potential to serve as models for the study of compartmentalization as well as biomineralization in bacteria. Additionally, they offer the opportunity to design applications that take advantage of the particular properties of magnetosomes. In recent years, a sustained effort to identify the molecular basis of this process has resulted in a clearer understanding of the magnetosome formation and biomineralization. Here, I present an overview of MB and explore the possible molecular mechanisms of membrane remodeling, protein sorting, cytoskeletal organization, iron transport, and biomineralization that lead to the formation of a functional magnetosome organelle.
Collapse
Affiliation(s)
- Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
39
|
Postec A, Tapia N, Bernadac A, Joseph M, Davidson S, Wu LF, Ollivier B, Pradel N. Magnetotactic bacteria in microcosms originating from the French Mediterranean Coast subjected to oil industry activities. MICROBIAL ECOLOGY 2012; 63:1-11. [PMID: 21766218 DOI: 10.1007/s00248-011-9910-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/30/2011] [Indexed: 05/31/2023]
Abstract
Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.
Collapse
Affiliation(s)
- Anne Postec
- IRD, UMR_D 180, Université Aix Marseille, ESIL case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Newly isolated but uncultivated magnetotactic bacterium of the phylum Nitrospirae from Beijing, China. Appl Environ Microbiol 2011; 78:668-75. [PMID: 22113917 DOI: 10.1128/aem.06764-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments.
Collapse
|
41
|
Kolinko S, Jogler C, Katzmann E, Wanner G, Peplies J, Schüler D. Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3. Environ Microbiol 2011; 14:1709-21. [PMID: 22003954 DOI: 10.1111/j.1462-2920.2011.02609.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magnetotactic bacteria (MTB) are a diverse group of prokaryotes that orient along magnetic fields using membrane-coated magnetic nanocrystals of magnetite (Fe(3) O(4) ) or greigite (Fe(3) S(4) ), the magnetosomes. Previous phylogenetic analysis of MTB has been limited to few cultivated species and most abundant members of natural populations, which were assigned to Proteobacteria and the Nitrospirae phyla. Here, we describe a single cell-based approach that allowed the targeted phylogenetic and ultrastructural analysis of the magnetotactic bacterium SKK-01, which was low abundant in sediments of Lake Chiemsee. Morphologically conspicuous single cells of SKK-01 were micromanipulated from magnetically collected multi-species MTB populations, which was followed by whole genome amplification and ultrastructural analysis of sorted cells. Besides intracellular sulphur inclusions, the large ovoid cells of SKK-01 harbour ∼175 bullet-shaped magnetosomes arranged in multiple chains that consist of magnetite as revealed by TEM and EDX analysis. Sequence analysis of 16 and 23S rRNA genes from amplified genomic DNA as well as fluorescence in situ hybridization assigned SKK-01 to the candidate division OP3, which so far lacks any cultivated representatives. SKK-01 represents the first morphotype that can be assigned to the OP3 group as well as the first magnetotactic member of the PVC superphylum.
Collapse
Affiliation(s)
- Sebastian Kolinko
- Ludwig-Maximilians-Universität Munich, Microbiology, Großhaderner Strasse 2-4, Planegg-Martinsried, Germany
| | | | | | | | | | | |
Collapse
|
42
|
Lin W, Wang Y, Li B, Pan Y. A biogeographic distribution of magnetotactic bacteria influenced by salinity. ISME JOURNAL 2011; 6:475-9. [PMID: 21866181 DOI: 10.1038/ismej.2011.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Magnetotactic bacteria (MTB), which synthesize intracellular ferromagnetic magnetite and/or greigite magnetosomes, have significant roles in global iron cycling in aquatic systems, as well as sedimentary magnetism. The occurrence of MTB has been reported in aquatic environments from freshwater to marine ecosystems; however, the distribution of MTB across heterogeneous habitats remains unclear. Here we examined the MTB communities from diverse habitats across northern and southern China, using comprehensive transmission electron microscopy and comparison of 16S rRNA gene analyses. A total of 334 16S rRNA gene sequences were analyzed, representing the most comprehensive analysis on the diversity and distribution of MTB to date. The majority (95%) of sequences belong to the Alphaproteobacteria, whereas a population of giant magnetotactic rod is affiliated with the Nitrospirae phylum. By a statistical comparison of these sequence data and publicly available MTB sequences, we infer for the first time that the composition of MTB communities represents a biogeographic distribution across globally heterogeneous environments, which is influenced by salinity.
Collapse
Affiliation(s)
- Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.
| | | | | | | |
Collapse
|
43
|
Frequent mutations within the genomic magnetosome island of Magnetospirillum gryphiswaldense are mediated by RecA. J Bacteriol 2011; 193:5328-34. [PMID: 21821768 DOI: 10.1128/jb.05491-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes.
Collapse
|
44
|
Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branching Nitrospira phylum. Proc Natl Acad Sci U S A 2010; 108:1134-9. [PMID: 21191098 DOI: 10.1073/pnas.1012694108] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a phylogenetically diverse group which uses intracellular membrane-enclosed magnetite crystals called magnetosomes for navigation in their aquatic habitats. Although synthesis of these prokaryotic organelles is of broad interdisciplinary interest, its genetic analysis has been restricted to a few closely related members of the Proteobacteria, in which essential functions required for magnetosome formation are encoded within a large genomic magnetosome island. However, because of the lack of cultivated representatives from other phyla, it is unknown whether the evolutionary origin of magnetotaxis is monophyletic, and it has been questioned whether homologous mechanisms and structures are present in unrelated MTB. Here, we present the analysis of the uncultivated "Candidatus Magnetobacterium bavaricum" from the deep branching Nitrospira phylum by combining micromanipulation and whole genome amplification (WGA) with metagenomics. Target-specific sequences obtained by WGA of cells, which were magnetically collected and individually sorted from sediment samples, were used for PCR screening of metagenomic libraries. This led to the identification of a genomic cluster containing several putative magnetosome genes with homology to those in Proteobacteria. A variety of advanced electron microscopic imaging tools revealed a complex cell envelope and an intricate magnetosome architecture. The presence of magnetosome membranes as well as cytoskeletal magnetosome filaments suggests a similar mechanism of magnetosome formation in "Cand. M. bavaricum" as in Proteobacteria. Altogether, our findings suggest a monophyletic origin of magnetotaxis, and relevant genes were likely transferred horizontally between Proteobacteria and representatives of the Nitrospira phylum.
Collapse
|
45
|
Metagenomic analysis reveals unexpected subgenomic diversity of magnetotactic bacteria within the phylum Nitrospirae. Appl Environ Microbiol 2010; 77:323-6. [PMID: 21057016 DOI: 10.1128/aem.01476-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A targeted metagenomic approach was applied to investigate magnetotactic bacteria (MTB) within the phylum Nitrospirae in Lake Miyun near Beijing, China. Five fosmids containing rRNA operons were identified. Comparative sequence analysis of a total of 172 kb provided new insights into their genome organization and revealed unexpected subgenomic diversity of uncultivated MTB in the phylum Nitrospirae. In addition, affiliation of two novel MTB with the phylum Nitrospirae was verified by fluorescence in situ hybridization. One of them was morphologically similar to "Candidatus Magnetobacterium bavaricum," but the other differed substantially in cell shape and magnetosome organization from all previously described "Ca. Magnetobacterium bavaricum"-like bacteria.
Collapse
|
46
|
Lefèvre CT, Frankel RB, Abreu F, Lins U, Bazylinski DA. Culture-independent characterization of a novel, uncultivated magnetotactic member of the Nitrospirae phylum. Environ Microbiol 2010; 13:538-49. [PMID: 20977572 DOI: 10.1111/j.1462-2920.2010.02361.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A magnetotactic bacterium, designated strain LO-1, of the Nitrospirae phylum was detected and concentrated from a number of freshwater and slightly brackish aquatic environments in southern Nevada. The closest phylogenetic relative to LO-1 is Candidatus Magnetobacterium bavaricum based on a 91.2% identity in their 16S rRNA gene sequence. Chemical and cell profiles of a microcosm containing water and sediment show that cells of strain LO-1 are confined to the oxic-anoxic interface and the upper regions of the anaerobic zone which in this case, occurred in the sediment. This microorganism is relatively large, ovoid in morphology and usually biomineralizes three braid-like bundles of multiple chains of bullet-shaped magnetosomes that appeared to be enclosed in a magnetosome membrane. Cells of LO-1 had an unusual three-layered unit membrane cell wall and contained several types of inclusions, some of which are sulfur-rich. Strain LO-1 is motile by means of a single bundle of sheathed flagella and exhibits the typical 'wobbling' motility and helical swimming ('flight') path of the magnetotactic cocci. This study and reports from others suggest that LO-1-like organisms are widespread in sediments of freshwater to brackish natural aquatic environments.
Collapse
Affiliation(s)
- Christopher T Lefèvre
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV 89154-4004, USA
| | | | | | | | | |
Collapse
|