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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.
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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.
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Karlicki M, Bednarska A, Hałakuc P, Maciszewski K, Karnkowska A. Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. FEMS Microbiol Ecol 2024; 100:fiae104. [PMID: 39039016 DOI: 10.1093/femsec/fiae104] [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: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Bednarska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
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3
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Medina-Ruiz A, Jiménez-Millán J, Abad I, Gálvez A, Grande MJ, Jiménez-Espinosa R. Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171362. [PMID: 38428615 DOI: 10.1016/j.scitotenv.2024.171362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.
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Affiliation(s)
- Antonio Medina-Ruiz
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Juan Jiménez-Millán
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - Isabel Abad
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Antonio Gálvez
- Microbiology Division, Department of Health Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - María José Grande
- Microbiology Division, Department of Health Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Rosario Jiménez-Espinosa
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
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Yang J, Zhang S, Zhang Y, Zhao D, Liu T, Sun X, Yan L. Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe 3O 4 nanoparticles in Acidithiobacillus ferrooxidans BYM. Microbiol Spectr 2023; 11:e0172923. [PMID: 37800960 PMCID: PMC10714799 DOI: 10.1128/spectrum.01729-23] [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: 04/26/2023] [Accepted: 08/17/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.
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Affiliation(s)
- Jiani Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yu Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang, China
| | - Xindi Sun
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing, Heilongjiang, China
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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Cosmidis J. Will tomorrow's mineral materials be grown? Microb Biotechnol 2023; 16:1713-1722. [PMID: 37522764 PMCID: PMC10443349 DOI: 10.1111/1751-7915.14298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023] Open
Abstract
Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.
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Affiliation(s)
- Julie Cosmidis
- Department of Earth SciencesUniversity of OxfordOxfordUK
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7
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Awal RP, Lefevre CT, Schüler D. Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense. mBio 2023; 14:e0328222. [PMID: 37318230 PMCID: PMC10470508 DOI: 10.1128/mbio.03282-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/03/2023] [Indexed: 06/16/2023] Open
Abstract
Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.
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Affiliation(s)
- Ram Prasad Awal
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Christopher T. Lefevre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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8
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Nakano S, Furutani H, Kato S, Kouduka M, Yamazaki T, Suzuki Y. Bullet-shaped magnetosomes and metagenomic-based magnetosome gene profiles in a deep-sea hydrothermal vent chimney. Front Microbiol 2023; 14:1174899. [PMID: 37440886 PMCID: PMC10335762 DOI: 10.3389/fmicb.2023.1174899] [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: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 07/15/2023] Open
Abstract
Magnetosome-producing microorganisms can sense and move toward the redox gradient and have been extensively studied in terrestrial and shallow marine sediment environments. However, given the difficulty of sampling, magnetotactic bacteria (MTB) are poorly explored in deep-sea hydrothermal fields. In this study, a deep-sea hydrothermal vent chimney from the Southern Mariana Trough was collected using a remotely operated submersible. The mineralogical and geochemical characterization of the vent chimney sample showed an internal iron redox gradient. Additionally, the electron microscopy of particles collected by magnetic separation from the chimney sample revealed MTB cells with bullet-shaped magnetosomes, and there were minor occurrences of cuboctahedral and hexagonal prismatic magnetosomes. Genome-resolved metagenomic analysis was performed to identify microorganisms that formed magnetosomes. A metagenome-assembled genome (MAG) affiliated with Nitrospinae had magnetosome genes such as mamA, mamI, mamM, mamP, and mamQ. Furthermore, a diagnostic feature of MTB genomes, such as magnetosome gene clusters (MGCs), including mamA, mamP, and mamQ, was also confirmed in the Nitrospinae-affiliated MAG. Two lines of evidence support the occurrence of MTB in a deep-sea, inactive hydrothermal vent environment.
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Affiliation(s)
- Shinsaku Nakano
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Furutani
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Mariko Kouduka
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Toshitsugu Yamazaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
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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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10
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Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nat Microbiol 2023; 8:727-744. [PMID: 36928026 PMCID: PMC10066038 DOI: 10.1038/s41564-022-01319-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023]
Abstract
Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
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11
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de Souza Cabral A, Verdan M, Presciliano R, Silveira F, Correa T, Abreu F. Large-Scale Cultivation of Magnetotactic Bacteria and the Optimism for Sustainable and Cheap Approaches in Nanotechnology. Mar Drugs 2023; 21:60. [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] [MESH Headings] [Grants] [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.
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Affiliation(s)
| | | | | | | | | | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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12
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Liu P, Zheng Y, Zhang R, Bai J, Zhu K, Benzerara K, Menguy N, Zhao X, Roberts AP, Pan Y, Li J. Key gene networks that control magnetosome biomineralization in magnetotactic bacteria. Natl Sci Rev 2022; 10:nwac238. [PMID: 36654913 PMCID: PMC9840458 DOI: 10.1093/nsr/nwac238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 01/21/2023] Open
Abstract
Magnetotactic bacteria (MTB) are a group of phylogenetically and morphologically diverse prokaryotes that have the capability of sensing Earth's magnetic field via nanocrystals of magnetic iron minerals. These crystals are enclosed within intracellular membranes or organelles known as magnetosomes and enable a sensing function known as magnetotaxis. Although MTB were discovered over half a century ago, the study of the magnetosome biogenesis and organization remains limited to a few cultured MTB strains. Here, we present an integrative genomic and phenomic analysis to investigate the genetic basis of magnetosome biomineralization in both cultured and uncultured strains from phylogenetically diverse MTB groups. The magnetosome gene contents/networks of strains are correlated with magnetic particle morphology and chain configuration. We propose a general model for gene networks that control/regulate magnetosome biogenesis and chain assembly in MTB systems.
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Affiliation(s)
| | | | - Rongrong Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinling Bai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kelei Zhu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris 75005, France
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris 75005, France
| | - 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
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Bärenstrauch M, Vanhove AS, Allégra S, Peuble S, Gallice F, Paran F, Lavastre V, Girardot F. Microbial diversity and geochemistry of groundwater impacted by steel slag leachates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156987. [PMID: 35772557 DOI: 10.1016/j.scitotenv.2022.156987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m3 steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.
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Affiliation(s)
- Margot Bärenstrauch
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Audrey S Vanhove
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Séverine Allégra
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Steve Peuble
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Gallice
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Paran
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Véronique Lavastre
- Université de Lyon, Université Jean Monnet Saint-Etienne, Laboratoire de Géologie de Lyon - Terre Planètes Environnement LGL-TPE, CNRS -UMR 5276, F-42023 Saint-Etienne, France
| | - Françoise Girardot
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France.
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14
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Shimoshige H, Kobayashi H, Shimamura S, Miyazaki M, Maekawa T. Fundidesulfovibrio magnetotacticus sp. nov., a sulphate-reducing magnetotactic bacterium, isolated from sediments and freshwater of a pond. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A sulphate-reducing magnetotactic bacterium, designated strain FSS-1T, was isolated from sediments and freshwater of Suwa Pond located in Hidaka, Saitama, Japan. Strain FSS-1T was a motile, Gram-negative and curved rod-shaped bacterium that synthesizes bullet-shaped magnetite (Fe3O4) nanoparticles in each cell. Strain FSS-1T was able to grow in the range of pH 6.5–8.0 (optimum, pH 7.0), 22–34 °C (optimum, 28 °C) and with 0–8.0 g l−1 NaCl (optimum, 0–2.0 g l−1 NaCl). Strain FSS-1T grew well in the presence of 50 µM ferric quinate as an iron source. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The major menaquinone was MK-7 (H2). Strain FSS-1T contained desulfoviridin, cytochrome c
3 and catalase, but did not contain oxidase. Strain FSS-1T used fumarate, lactate, pyruvate, malate, formate/acetate, succinate, tartrate, ethanol, 1-propanol, peptone, soytone and yeast extract as electron donors, while the strain used sulphate, thiosulphate and fumarate as electron acceptors. Fumarate was fermented in the absence of electron acceptors. Analysis of the 16S rRNA gene sequence showed that strain FSS-1T is a member of the genus
Fundidesulfovibrio
. The gene sequence showed 96.7, 95.0, 92.0, 91.2 and 91.4% similarities to the most closely related members of the genera
Fundidesulfovibrio putealis
B7-43T,
Fundidesulfovibrio butyratiphilus
BSYT,
Desulfolutivibrio sulfoxidireducens
DSM 107105T,
Desulfolutivibrio sulfodismutans
ThAc01T and
Solidesulfovibrio magneticus
RS-1T, respectively. The DNA G+C content of strain FSS-1T was 67.5 mol%. The average nucleotide identity value between strain FSS-1T and
F. putealis
B7-43T was 80.7 %. Therefore, strain FSS-1T represents a novel species within the genus
Fundidesulfovibrio
, for which the name Fundidesulfovibrio magnetotacticus sp. nov. is proposed (=JCM 32405T=DSM 110007T).
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Affiliation(s)
- Hirokazu Shimoshige
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Kanagawa 237-0061, Japan
| | - Hideki Kobayashi
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Shigeru Shimamura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Kanagawa 237-0061, Japan
| | - Toru Maekawa
- Graduate School of Interdisciplinary New Science, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350- 15 8585, Japan
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
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15
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Zimina TM, Sitkov NO, Gareev KG, Fedorov V, Grouzdev D, Koziaeva V, Gao H, Combs SE, Shevtsov M. Biosensors and Drug Delivery in Oncotheranostics Using Inorganic Synthetic and Biogenic Magnetic Nanoparticles. BIOSENSORS 2022; 12:789. [PMID: 36290927 PMCID: PMC9599632 DOI: 10.3390/bios12100789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Tatiana M. Zimina
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Nikita O. Sitkov
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Kamil G. Gareev
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Viacheslav Fedorov
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Denis Grouzdev
- SciBear OU, Tartu mnt 67/1-13b, Kesklinna Linnaosa, 10115 Tallinn, Estonia
| | - Veronika Koziaeva
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia
| | - Huile Gao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Stephanie E. Combs
- Department of Radiation Oncology, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Maxim Shevtsov
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
- Department of Radiation Oncology, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
- National Center for Neurosurgery, Nur-Sultan 010000, Kazakhstan
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16
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Perez‐Molphe‐Montoya E, Küsel K, Overholt WA. Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota. Environ Microbiol 2022; 24:5437-5449. [DOI: 10.1111/1462-2920.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kirsten Küsel
- Institute of Biodiversity Friedrich Schiller University Jena Germany
- The German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐ Leipzig Germany
| | - Will A. Overholt
- Institute of Biodiversity Friedrich Schiller University Jena Germany
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17
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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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18
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Li J, Liu P, Menguy N, Benzerara K, Bai J, Zhao X, Leroy E, Zhang C, Zhang H, Liu J, Zhang R, Zhu K, Roberts AP, Pan Y. Identification of sulfate-reducing magnetotactic bacteria via a group-specific 16S rDNA primer and correlative fluorescence and electron microscopy: strategy for culture-independent study. Environ Microbiol 2022; 24:5019-5038. [PMID: 35726890 DOI: 10.1111/1462-2920.16109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/02/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022]
Abstract
Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities. However, incomplete coverage and amplification biases inevitably prevent detection of some phylogenetically specific or non-abundant MTB. Here, we propose a new formulation of the upstream 390F primer that we combined with the downstream 1492R primer to specifically amplify 1,100-bp 16S rRNA gene sequences of sulfate-reducing MTB in freshwater sediments from Lake Weiyanghu, Xi'an, northwestern China. With correlative fluorescence in situ hybridization and scanning/transmission electron microscopy, three novel MTB strains (WYHR-2, WYHR-3, and WYHR-4) from the Desulfobacterota phylum were identified phylogenetically and structurally at the single cell level. Strain WYHR-2 produces bullet-shaped magnetosome magnetite, while the other two strains produce both cubic/prismatic greigite and bullet-shaped magnetite. Our results expand knowledge of bacterial diversity and magnetosome biomineralization of sulfate-reducing MTB. We also propose a general strategy for identifying and characterizing uncultured MTB from natural environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Jinling Bai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | - Eric Leroy
- ICMPE, University Paris East, UMR 7182, CNRS, 2-8 rue Henri Dunant, Thiais Cedex, France
| | - Chaoqun Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Heng Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jiawei Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongrong Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Keilei Zhu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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19
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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.
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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.
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20
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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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21
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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]
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22
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Amor M, Wan J, Egli R, Carlut J, Gatel C, Andersen IM, Snoeck E, Komeili A. Key Signatures of Magnetofossils Elucidated by Mutant Magnetotactic Bacteria and Micromagnetic Calculations. JOURNAL OF GEOPHYSICAL RESEARCH. SOLID EARTH 2022; 127:e2021JB023239. [PMID: 35444924 PMCID: PMC9017866 DOI: 10.1029/2021jb023239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Magnetotactic bacteria (MTB) produce single-stranded or multi-stranded chains of magnetic nanoparticles that contribute to the magnetization of sediments and rocks. Their magnetic fingerprint can be detected in ancient geological samples and serve as a unique biosignature of microbial life. However, some fossilized assemblages bear contradictory signatures pointing to magnetic components that have distinct origin(s). Here, using micromagnetic simulations and mutant MTB producing looped magnetosome chains, we demonstrate that the observed magnetofossil fingerprints are produced by a mixture of single-stranded and multi-stranded chains, and that diagenetically induced chain collapse, if occurring, must preserve the strong uniaxial anisotropy of native chains. This anisotropy is the key factor for distinguishing magnetofossils from other populations of natural magnetite particles, including those with similar individual crystal characteristics. Furthermore, the detailed properties of magnetofossil signatures depend on the proportion of equant and elongated magnetosomes, as well as on the relative abundances of single-stranded and multi-stranded chains. This work has important paleoclimatic, paleontological, and phylogenetic implications, as it provides reference data to differentiate distinct MTB lineages according to their chain and magnetosome morphologies, which will enable the tracking of the evolution of some of the most ancient biomineralizing organisms in a time-resolved manner. It also enables a more accurate discrimination of different sources of magnetite particles, which is pivotal for gaining better environmental and relative paleointensity reconstructions from sedimentary records.
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Affiliation(s)
- Matthieu Amor
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
- Aix‐Marseille Université, CEA, CNRS, BIAMSaint‐Paul‐lez‐DuranceFrance
| | - Juan Wan
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Ramon Egli
- Zentralanstalt für Meteorologie und Geodynamik (ZAMG)ViennaAustria
- Université de Paris, Institut de Physique du Globe de Paris, CNRSParisFrance
| | - Julie Carlut
- Université de Paris, Institut de Physique du Globe de Paris, CNRSParisFrance
| | | | | | | | - Arash Komeili
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
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23
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Pohl A, Young SAE, Schmitz TC, Farhadi D, Zarivach R, Faivre D, Blank KG. Magnetite-binding proteins from the magnetotactic bacterium Desulfamplus magnetovallimortis BW-1. NANOSCALE 2021; 13:20396-20400. [PMID: 34860229 DOI: 10.1039/d1nr04870h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Magnetite-binding proteins are in high demand for the functionalization of magnetic nanoparticles. Binding analysis of six previously uncharacterized proteins from the magnetotactic Deltaproteobacterium Desulfamplus magnetovallimortis BW-1 identified two new magnetite-binding proteins (Mad10, Mad11). These proteins can be utilized as affinity tags for the immobilization of recombinant fusion proteins to magnetite.
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Affiliation(s)
- Anna Pohl
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Sarah A E Young
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Tara C Schmitz
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Daniel Farhadi
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Raz Zarivach
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Damien Faivre
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul lez Durance, France
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476 Potsdam, Germany.
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24
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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25
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Williams TJ, Allen MA, Berengut JF, Cavicchioli R. Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake. Front Microbiol 2021; 12:741077. [PMID: 34707591 PMCID: PMC8542988 DOI: 10.3389/fmicb.2021.741077] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial "dark matter" taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
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26
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Degenhardt J, Merder J, Heyerhoff B, Simon H, Engelen B, Waska H. Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. Microorganisms 2021; 9:1720. [PMID: 34442799 PMCID: PMC8399146 DOI: 10.3390/microorganisms9081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.
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Affiliation(s)
- Julius Degenhardt
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Julian Merder
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Hannelore Waska
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
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27
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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.
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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
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28
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Evolution of default genetic control mechanisms. PLoS One 2021; 16:e0251568. [PMID: 33984070 PMCID: PMC8118313 DOI: 10.1371/journal.pone.0251568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. The model was run 118 times to an average of 1.4∙106 ‘generations’ each with a range of starting parameters probed the conditions under which genomes evolved a ‘default style’ of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active (‘default on’), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated (‘default off’ logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a ‘default off’ mode.
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29
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Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881984 DOI: 10.1099/ijsem.0.004671] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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30
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Liu P, Tamaxia A, Liu Y, Qiu H, Pan J, Jin Z, Zhao X, Roberts AP, Pan Y, Li J. Identification and characterization of magnetotactic Gammaproteobacteria from a salt evaporation pool, Bohai Bay, China. Environ Microbiol 2021; 24:938-950. [PMID: 33876543 DOI: 10.1111/1462-2920.15516] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 11/27/2022]
Abstract
Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that can produce intracellular chain-assembled nanocrystals of magnetite (Fe3 O4 ) or greigite (Fe3 S4 ). Compared with their wide distribution in the Alpha-, Eta- and Delta-proteobacteria classes, few MTB strains have been identified in the Gammaproteobacteria class, resulting in limited knowledge of bacterial diversity and magnetosome biomineralization within this phylogenetic branch. Here, we identify two magnetotactic Gammaproteobacteria strains (tentatively named FZSR-1 and FZSR-2 respectively) from a salt evaporation pool in Bohai Bay, at the Fuzhou saltern, Dalian City, eastern China. Phylogenetic analysis indicates that strain FZSR-2 is the same species as strains SHHR-1 and SS-5, which were discovered previously from brackish and hypersaline environments respectively. Strain FZSR-1 represents a novel species. Compared with strains FZSR-2, SHHR-1 and SS-5 in which magnetite particles are assembled into a single chain, FZSR-1 cells form relatively narrower magnetite nanoparticles that are often organized into double chains. We find a good relationship between magnetite morphology within strains FZSR-2, SHHR-1 and SS-5 and the salinity of the environment in which they live. This study expands the bacterial diversity of magnetotactic Gammaproteobacteria and provides new insights into magnetosome biomineralization within magnetotactic Gammaproteobacteria.
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Affiliation(s)
- Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Alima Tamaxia
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Qiu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juntong Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongke Jin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary 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
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Shimoshige H, Kobayashi H, Shimamura S, Mizuki T, Inoue A, Maekawa T. Isolation and cultivation of a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio. PLoS One 2021; 16:e0248313. [PMID: 33705469 PMCID: PMC7951924 DOI: 10.1371/journal.pone.0248313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/23/2021] [Indexed: 11/19/2022] Open
Abstract
Magnetotactic bacteria (MTB) synthesize magnetosomes composed of membrane-enveloped magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles in the cells. It is known that the magnetotactic Deltaproteobacteria are ubiquitous and inhabit worldwide in the sediments of freshwater and marine environments. Mostly known MTB belonging to the Deltaproteobacteria are dissimilatory sulfate-reducing bacteria that biomineralize bullet-shaped magnetite nanoparticles, but only a few axenic cultures have been obtained so far. Here, we report the isolation, cultivation and characterization of a dissimilatory sulfate-reducing magnetotactic bacterium, which we designate “strain FSS-1”. We found that the strain FSS-1 is a strict anaerobe and uses casamino acids as electron donors and sulfate as an electron acceptor to reduce sulfate to hydrogen sulfide. The strain FSS-1 produced bullet-shaped magnetite nanoparticles in the cells and responded to external magnetic fields. On the basis of 16S rRNA gene sequence analysis, the strain FSS-1 is a member of the genus Desulfovibrio, showing a 96.7% sequence similarity to Desulfovibrio putealis strain B7-43T. Futhermore, the magnetosome gene cluster of strain FSS-1 was different from that of Desulfovibrio magneticus strain RS-1. Thus, the strain FSS-1 is considered to be a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio.
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Affiliation(s)
- Hirokazu Shimoshige
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
- * E-mail: (TM); (HS)
| | - Hideki Kobayashi
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Toru Mizuki
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
| | - Akira Inoue
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
| | - Toru Maekawa
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama, Japan
- * E-mail: (TM); (HS)
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32
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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.
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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
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33
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Tan SM, Ismail MH, Cao B. Biodiversity of magnetotactic bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis. ENVIRONMENTAL RESEARCH 2021; 194:110714. [PMID: 33422504 DOI: 10.1016/j.envres.2021.110714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/22/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Abstract
Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (~0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.
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Affiliation(s)
- Shi Ming Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, N1-01C-69, 639798, Singapore.
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34
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Vavourakis CD, Heijnen L, Peters MCFM, Marang L, Ketelaars HAM, Hijnen WAM. Spatial and Temporal Dynamics in Attached and Suspended Bacterial Communities in Three Drinking Water Distribution Systems with Variable Biological Stability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14535-14546. [PMID: 33135888 DOI: 10.1021/acs.est.0c04532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial presence and regrowth in drinking water distribution systems (DWDSs) is routinely monitored to assess the biological stability of drinking water without a residual disinfectant, but the conventional microbiological culture methods currently used target only a very small fraction of the complete DWDS microbiome. Here, we sequenced 16S rRNA gene amplicons to elucidate the attached and suspended prokaryotic community dynamics within three nonchlorinated DWDSs with variable regrowth conditions distributing similarly treated surface water from the same source. One rural location, with less regrowth related issues, differed most strikingly from the other two urban locations by the exclusive presence of Pseudonocardia (Actinobacteria) in the biofilm and the absence of Limnobacter (Betaproteobacteriales) in the water and loose deposits during summer. There was a dominant seasonal effect on the drinking water microbiomes at all three locations. For one urban location, it was established that the most significant changes in the microbial community composition on a spatial scale occurred shortly after freshly treated water entered the DWDS. However, summerly regrowth of Limnobacter, one of the dominant genera in the distributed drinking water, already occurred in the clean water reservoir at the treatment plant before further distribution. The highlighted bacterial lineages within these highly diverse DWDS communities might be important new indicators for undesirable regrowth conditions affecting the final drinking water quality.
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Affiliation(s)
| | - Leo Heijnen
- KWR Watercycle Research Institute, Groningenhaven 7, 3433PE Nieuwegein, The Netherlands
| | | | - Leonie Marang
- Evides Water Company, P.O. Box 4472, 3006 AL, Rotterdam, The Netherlands
| | - Henk A M Ketelaars
- Evides Water Company, P.O. Box 4472, 3006 AL, Rotterdam, The Netherlands
| | - Wim A M Hijnen
- Evides Water Company, P.O. Box 4472, 3006 AL, Rotterdam, The Netherlands
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35
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Cabrol L, Thalasso F, Gandois L, Sepulveda-Jauregui A, Martinez-Cruz K, Teisserenc R, Tananaev N, Tveit A, Svenning MM, Barret M. Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139588. [PMID: 32497884 DOI: 10.1016/j.scitotenv.2020.139588] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Arctic lakes emit methane (CH4) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH4 cycle in lakes, a crucial component of the global CH4 cycle.
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Affiliation(s)
- Léa Cabrol
- Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad de Valparaiso, Av Brasil 2085, Valparaiso, Chile
| | - Frédéric Thalasso
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Laure Gandois
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)2, Santiago, Chile
| | | | - Roman Teisserenc
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | | | - Alexander Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France.
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36
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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.
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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
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37
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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.
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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
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38
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Abstract
Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular compartments that bear many hallmarks of eukaryotic organelles. One unique and elegant group of organisms is at the forefront of studies into the mechanisms of organelle formation and biomineralization. Magnetotactic bacteria (MTB) produce organelles called magnetosomes that contain nanocrystals of magnetic material, and understanding the molecular mechanisms behind magnetosome formation and biomineralization is a rich area of study. In this Review, we focus on the genetics behind the formation of magnetosomes and biomineralization. We cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB.
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Affiliation(s)
- Hayley C. McCausland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Arash Komeili
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
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39
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Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
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Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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40
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Magnetoreception in Microorganisms. Trends Microbiol 2019; 28:266-275. [PMID: 31753537 DOI: 10.1016/j.tim.2019.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 11/24/2022]
Abstract
Magnetoreception is the sense whereby organisms geolocate and navigate in response to the Earth's magnetic field lines. For decades, magnetotactic bacteria have been the only known magnetoreceptive microorganisms. The magnetotactic behaviour of these aquatic prokaryotes is due to the biomineralization of magnetic crystals. While an old report alleged the existence of microbial algae with similar behaviour, recent discoveries have demonstrated the existence of unicellular eukaryotes able to sense the geomagnetic field, and have revealed different mechanisms and strategies involved in such a sensing. Some ciliates can be magnetically guided after predation of magnetotactic bacteria, while some flagellates acquired this sense through symbiosis with magnetic bacteria. A report has even suggested that some magnetotactic protists could biomineralize magnetic crystals.
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Pohl A, Berger F, Sullan RMA, Valverde-Tercedor C, Freindl K, Spiridis N, Lefèvre CT, Menguy N, Klumpp S, Blank KG, Faivre D. Decoding Biomineralization: Interaction of a Mad10-Derived Peptide with Magnetite Thin Films. NANO LETTERS 2019; 19:8207-8215. [PMID: 31565946 DOI: 10.1021/acs.nanolett.9b03560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein-surface interactions play a pivotal role in processes as diverse as biomineralization, biofouling, and the cellular response to medical implants. In biomineralization processes, biomacromolecules control mineral deposition and architecture via complex and often unknown mechanisms. For studying these mechanisms, the formation of magnetite nanoparticles in magnetotactic bacteria has become an excellent model system. Most interestingly, nanoparticle morphologies have been discovered that defy crystallographic rules (e.g., in the species Desulfamplus magnetovallimortis strain BW-1). In certain conditions, this strain mineralizes bullet-shaped magnetite nanoparticles, which exhibit defined (111) crystal faces and are elongated along the [100] direction. We hypothesize that surface-specific protein interactions break the nanoparticle symmetry, inhibiting the growth of certain crystal faces and thereby favoring the growth of others. Screening the genome of BW-1, we identified Mad10 (Magnetosome-associated deep-branching) as a potential magnetite-binding protein. Using atomic force microscope (AFM)-based single-molecule force spectroscopy, we show that a Mad10-derived peptide, which represents the most conserved region of Mad10, binds strongly to (100)- and (111)-oriented single-crystalline magnetite thin films. The peptide-magnetite interaction is thus material- but not crystal-face-specific. It is characterized by broad rupture force distributions that do not depend on the retraction speed of the AFM cantilever. To account for these experimental findings, we introduce a three-state model that incorporates fast rebinding. The model suggests that the peptide-surface interaction is strong in the absence of load, which is a direct result of this fast rebinding process. Overall, our study sheds light on the kinetic nature of peptide-surface interactions and introduces a new magnetite-binding peptide with potential use as a functional coating for magnetite nanoparticles in biotechnological and biomedical applications.
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Affiliation(s)
- Anna Pohl
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
- Mechano(bio)chemistry , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Florian Berger
- Laboratory of Sensory Neuroscience , The Rockefeller University , 1230 York Avenue , New York 10065 , United States
| | - Ruby M A Sullan
- Mechano(bio)chemistry , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Carmen Valverde-Tercedor
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Kinga Freindl
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , Niezapominajek 8 , 30-239 Krakow , Poland
| | - Nika Spiridis
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , Niezapominajek 8 , 30-239 Krakow , Poland
| | | | - Nicolas Menguy
- Sorbonne Université , UMR CNRS 7590, IRD. MNHN, Institut de Minéralogie, Physique des Matériaux et Cosmochimie - IMPMC , 4 Place Jussieu , 75005 Paris , France
| | - Stefan Klumpp
- Department of Theory & Bio-Systems , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
- Institute for the Dynamics of Complex Systems , University of Göttingen , Friedrich Hund Platz 1 , 37077 Göttingen , Germany
| | - Kerstin G Blank
- Mechano(bio)chemistry , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Damien Faivre
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
- Aix-Marseille Université , CEA, CNRS, BIAM, 13108 Saint Paul lez Durance , France
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Pan H, Dong Y, Teng Z, Li J, Zhang W, Xiao T, Wu LF. A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom. FEMS Microbiol Lett 2019; 366:5681391. [PMID: 31855240 DOI: 10.1093/femsle/fnz253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of MTB. We propose that deltaproteobacterial MTB may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.
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Affiliation(s)
- Hongmiao Pan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China
| | - Yi Dong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China
| | - Zhaojie Teng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Jinhua Li
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, 19 Beitucheng Western Road, Beijing, 100029, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China
| | - Wenyan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China
| | - Tian Xiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, 7 Nanhai Road, Qingdao, 266071, China.,LCB, Aix-Marseille Univ, CNRS, 31 Chemin Joseph Aiguier, Marseille, 13402, France
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Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria. mSystems 2019; 4:4/5/e00315-19. [PMID: 31662428 PMCID: PMC6819731 DOI: 10.1128/msystems.00315-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth's geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria IMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.
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Leão P, Le Nagard L, Yuan H, Cypriano J, Da Silva-Neto I, Bazylinski DA, Acosta-Avalos D, de Barros HL, Hitchcock AP, Lins U, Abreu F. Magnetosome magnetite biomineralization in a flagellated protist: evidence for an early evolutionary origin for magnetoreception in eukaryotes. Environ Microbiol 2019; 22:1495-1506. [PMID: 31188524 DOI: 10.1111/1462-2920.14711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 11/30/2022]
Abstract
The most well-recognized magnetoreception behaviour is that of the magnetotactic bacteria (MTB), which synthesize membrane-bounded magnetic nanocrystals called magnetosomes via a biologically controlled process. The magnetic minerals identified in prokaryotic magnetosomes are magnetite (Fe3 O4 ) and greigite (Fe3 S4 ). Magnetosome crystals, regardless of composition, have consistent, species-specific morphologies and single-domain size range. Because of these features, magnetosome magnetite crystals possess specific properties in comparison to abiotic, chemically synthesized magnetite. Despite numerous discoveries regarding MTB phylogeny over the last decades, this diversity is still considered underestimated. Characterization of magnetotactic microorganisms is important as it might provide insights into the origin and establishment of magnetoreception in general, including eukaryotes. Here, we describe the magnetotactic behaviour and characterize the magnetosomes from a flagellated protist using culture-independent methods. Results strongly suggest that, unlike previously described magnetotactic protists, this flagellate is capable of biomineralizing its own anisotropic magnetite magnetosomes, which are aligned in complex aggregations of multiple chains within the cell. This organism has a similar response to magnetic field inversions as MTB. Therefore, this eukaryotic species might represent an early origin of magnetoreception based on magnetite biomineralization. It should add to the definition of parameters and criteria to classify biogenic magnetite in the fossil record.
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Affiliation(s)
- Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Le Nagard
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Hao Yuan
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Inácio Da Silva-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, USA
| | | | | | - Adam P Hitchcock
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Phylogenetic and Structural Identification of a Novel Magnetotactic Deltaproteobacteria Strain, WYHR-1, from a Freshwater Lake. Appl Environ Microbiol 2019; 85:AEM.00731-19. [PMID: 31053584 DOI: 10.1128/aem.00731-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that are able to biomineralize intracellular, magnetic chains of magnetite or greigite nanocrystals called magnetosomes. Simultaneous characterization of MTB phylogeny and biomineralization is crucial but challenging because most MTB are extremely difficult to culture. We identify a large rod, bean-like MTB (tentatively named WYHR-1) from freshwater sediments of Weiyang Lake, Xi'an, China, using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Phylogenetic analysis of 16S rRNA gene sequences indicates that WYHR-1 is a novel genus from the Deltaproteobacteria class. Transmission electron microscope observations reveal that WYHR-1 cells contain tens of magnetite magnetosomes that are organized into a single chain bundle along the cell long axis. Mature WYHR-1 magnetosomes are bullet-shaped, straight, and elongated along the [001] direction, with a large flat end terminated by a {100} face at the base and a conical top. This crystal morphology is distinctively different from bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum. This indicates that WYHR-1 may have a different crystal growth process and mechanism from other species, which results from species-specific magnetosome biomineralization in MTB.IMPORTANCE Magnetotactic bacteria (MTB) represent a model system for understanding biomineralization and are also studied intensively in biogeomagnetic and paleomagnetic research. However, many uncultured MTB strains have not been identified phylogenetically or investigated structurally at the single-cell level, which limits comprehensive understanding of MTB diversity and their role in biomineralization. We have identified a novel MTB strain, WYHR-1, from a freshwater lake using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Our analyses further indicate that strain WYHR-1 represents a novel genus from the Deltaproteobacteria class. In contrast to bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum, WYHR-1 magnetosomes are bullet-shaped, straight, and highly elongated along the [001] direction, are terminated by a large {100} face at their base, and have a conical top. Our findings imply that, consistent with phylogenetic diversity of MTB, bullet-shaped magnetosomes have diverse crystal habits and growth patterns.
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Qin H, Wang S, Feng K, He Z, Virta MPJ, Hou W, Dong H, Deng Y. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. MICROBIOME 2019; 7:71. [PMID: 31054577 PMCID: PMC6500586 DOI: 10.1186/s40168-019-0688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 05/07/2023]
Abstract
Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
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Affiliation(s)
- Huayu Qin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhili He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China.
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 2019; 85:AEM.00110-19. [PMID: 30902854 DOI: 10.1128/aem.00110-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.IMPORTANCE Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.
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Effects of Single and Mixed Energy Sources on Intracellular Nanoparticles Synthesized by Acidithiobacillus ferrooxidans. MINERALS 2019. [DOI: 10.3390/min9030163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Effective biosynthesis of magnetite nanoparticles using current technology is challenging. We investigated the synthesis of nanoparticles by Acidithiobacillus ferrooxidans grown on ferrous iron, elemental sulphur, and mixtures of both substrates. A comparison of tests with different doping amounts of elemental sulphur in ferrous-containing medium showed that the addition of 0.25 and 0.5 M elemental sulphur to the medium resulted in an increased delay of microbial growth and ferrous iron oxidation. TEM suggested that the ferrous material was an essential energy source for the synthesis of nanoparticles in cells. TEM results indicated that the different ratios of ferrous and sulphur had no significant effect on the morphology of bacteria and the size of nanoparticles. High-resolution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDX), and X-ray absorption near edge structure (XANES) showed that the nanoparticles were composed of magnetite. For the first time, HRTEM and XANES spectra in-situ characterization was conducted to investigate the nanoparticles that were synthesized by A. ferrooxidans. The findings from this study indicated that the different ratios of ferrous and sulphur had no significant effect on size and shape of nanoparticles synthesized by A. ferrooxidans.
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Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst Appl Microbiol 2018; 42:85-93. [PMID: 30477901 DOI: 10.1016/j.syapm.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili. The organisms are predicted to be rod-shaped, slow-growers, with an anoxic, heterotrophic, and fermentative lifestyle. Predicted substrate utilization pattern includes multiple amino acids, dipeptides, tripeptides, and oligpopeptides; as well as few sugars. Predicted auxotrophies include proline, vitamin B6, lipoic acid, biotin, and vitamin B12. Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats. We propose the candidatus name Krumholzibacterium zodletonense gen. nov, sp. nov. for Zgenome0171T, with the genome serving as the type material for the novel family Krumholzibacteriaceae fam. nov., order Krumholzibacteriales ord. nov., class Krumholzibacteria class nov., and phylum Krumholzibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number QTKG01000000.
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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.
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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.
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