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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.
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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
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D'Angelo T, Goordial J, Lindsay MR, McGonigle J, Booker A, Moser D, Stepanauskus R, Orcutt BN. Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota. THE ISME JOURNAL 2023; 17:891-902. [PMID: 37012337 DOI: 10.1038/s41396-023-01397-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.
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Affiliation(s)
- Timothy D'Angelo
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Jacqueline Goordial
- University of Guelph, School of Environmental Sciences, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Melody R Lindsay
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
- Basepaws Pet Genetics, 1820 W. Carson Street, Suite 202-351, Torrance, CA, 90501, USA
| | - Anne Booker
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Duane Moser
- Desert Research Institute, 755 East Flamingo Road, Las Vegas, NV, 89119, USA
| | - Ramunas Stepanauskus
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA.
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Biosensors and Drug Delivery in Oncotheranostics Using Inorganic Synthetic and Biogenic Magnetic Nanoparticles. BIOSENSORS 2022; 12:bios12100789. [PMID: 36290927 PMCID: PMC9599632 DOI: 10.3390/bios12100789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
Abstract
Magnetic nanocarriers have attracted attention in translational oncology due to their ability to be employed both for tumor diagnostics and therapy. This review summarizes data on applications of synthetic and biogenic magnetic nanoparticles (MNPs) in oncological theranostics and related areas. The basics of both types of MNPs including synthesis approaches, structure, and physicochemical properties are discussed. The properties of synthetic MNPs and biogenic MNPs are compared with regard to their antitumor therapeutic efficiency, diagnostic potential, biocompatibility, and cellular toxicity. The comparative analysis demonstrates that both synthetic and biogenic MNPs could be efficiently used for cancer theranostics, including biosensorics and drug delivery. At the same time, reduced toxicity of biogenic particles was noted, which makes them advantageous for in vivo applications, such as drug delivery, or MRI imaging of tumors. Adaptability to surface modification based on natural biochemical processes is also noted, as well as good compatibility with tumor cells and proliferation in them. Advances in the bionanotechnology field should lead to the implementation of MNPs in clinical trials.
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Uzun M, Koziaeva V, Dziuba M, Leão P, Krutkina M, Grouzdev D. Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria. Front Microbiol 2022; 13:945734. [PMID: 35979495 PMCID: PMC9376291 DOI: 10.3389/fmicb.2022.945734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. Magnetotactic bacteria belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.
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Affiliation(s)
- Maria Uzun
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Veronika Koziaeva
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marina Dziuba
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Marine Science, The University of Texas at Austin, Austin, TX, United States
| | | | - Denis Grouzdev
- SciBear OU, Tallinn, Estonia
- *Correspondence: Denis Grouzdev,
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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: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [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.
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A Novel Isolate of Spherical Multicellular Magnetotactic Prokaryotes Has Two Magnetosome Gene Clusters and Synthesizes Both Magnetite and Greigite Crystals. Microorganisms 2022; 10:microorganisms10050925. [PMID: 35630369 PMCID: PMC9145555 DOI: 10.3390/microorganisms10050925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/10/2022] Open
Abstract
Multicellular magnetotactic prokaryotes (MMPs) are a unique group of magnetotactic bacteria that are composed of 10–100 individual cells and show coordinated swimming along magnetic field lines. MMPs produce nanometer-sized magnetite (Fe3O4) and/or greigite (Fe3S4) crystals—termed magnetosomes. Two types of magnetosome gene cluster (MGC) that regulate biomineralization of magnetite and greigite have been found. Here, we describe a dominant spherical MMP (sMMP) species collected from the intertidal sediments of Jinsha Bay, in the South China Sea. The sMMPs were 4.78 ± 0.67 μm in diameter, comprised 14–40 cells helical symmetrically, and contained bullet-shaped magnetite and irregularly shaped greigite magnetosomes. Two sets of MGCs, one putatively related to magnetite biomineralization and the other to greigite biomineralization, were identified in the genome of the sMMP, and two sets of paralogous proteins (Mam and Mad) that may function separately and independently in magnetosome biomineralization were found. Phylogenetic analysis indicated that the sMMPs were affiliated with Deltaproteobacteria. This is the first direct report of two types of magnetosomes and two sets of MGCs being detected in the same sMMP. The study provides new insights into the mechanism of biomineralization of magnetosomes in MMPs, and the evolutionary origin of MGCs.
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