1
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Ostrander CM, Shu Y, Nielsen SG, Dellwig O, Blusztajn J, Schulz-Vogt HN, Hübner V, Hansel CM. Anthropogenic Forcing of the Baltic Sea Thallium Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8510-8517. [PMID: 38695484 DOI: 10.1021/acs.est.4c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
Anthropogenic activities have fundamentally changed the chemistry of the Baltic Sea. According to results reported in this study, not even the thallium (Tl) isotope cycle is immune to these activities. In the anoxic and sulfidic ("euxinic") East Gotland Basin today, Tl and its two stable isotopes are cycled between waters and sediments as predicted based on studies of other redox-stratified basins (e.g., the Black Sea and Cariaco Trench). The Baltic seawater Tl isotope composition (ε205Tl) is, however, higher than predicted based on the results of conservative mixing calculations. Data from a short sediment core from East Gotland Basin demonstrates that this high seawater ε205Tl value originated sometime between about 1940 and 1947 CE, around the same time other prominent anthropogenic signatures begin to appear in the same core. This juxtaposition is unlikely to be coincidental and suggests that human activities in the surrounding area have altered the seawater Tl isotope mass-balance of the Baltic Sea.
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Affiliation(s)
- Chadlin M Ostrander
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yunchao Shu
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Sune G Nielsen
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Olaf Dellwig
- Department of Marine Geology, Leibniz Institute for Baltic Sea Research Warnemünde, IOW, 18119 Rostock, Germany
| | - Jerzy Blusztajn
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Heide N Schulz-Vogt
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, IOW, 18119 Rostock, Germany
| | - Vera Hübner
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Colleen M Hansel
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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2
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Yarahmadi A, Zare M, Aghayari M, Afkhami H, Jafari GA. Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future. Cell Commun Signal 2024; 22:239. [PMID: 38654309 PMCID: PMC11040964 DOI: 10.1186/s12964-024-01622-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Cancer, ranked as the second leading cause of mortality worldwide, leads to the death of approximately seven million people annually, establishing itself as one of the most significant health challenges globally. The discovery and identification of new anti-cancer drugs that kill or inactivate cancer cells without harming normal and healthy cells and reduce adverse effects on the immune system is a potential challenge in medicine and a fundamental goal in Many studies. Therapeutic bacteria and viruses have become a dual-faceted instrument in cancer therapy. They provide a promising avenue for cancer treatment, but at the same time, they also create significant obstacles and complications that contribute to cancer growth and development. This review article explores the role of bacteria and viruses in cancer treatment, examining their potential benefits and drawbacks. By amalgamating established knowledge and perspectives, this review offers an in-depth examination of the present research landscape within this domain and identifies avenues for future investigation.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Mitra Zare
- Department of Microbiology, Faculty of Sciences, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Masoomeh Aghayari
- Department of Microbiology, Faculty of Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.
| | - Gholam Ali Jafari
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
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3
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Yu W, Yang H, Chen J, Liao P, Wu J, Jiang L, Guo W. Molecular insights into the microbial degradation of sediment-derived DOM in a macrophyte-dominated lake under aerobic and hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170257. [PMID: 38253098 DOI: 10.1016/j.scitotenv.2024.170257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
The mineralization of dissolved organic matter (DOM) in sediments is an important factor leading to the eutrophication of macrophyte-dominated lakes. However, the changes in the molecular characteristics of sediment-derived DOM during microbial degradation in macrophyte-dominated lakes are not well understood. In this study, the microbial degradation process of sediment-derived DOM in Lake Caohai under aerobic and hypoxic conditions was investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics. The results revealed that the microbial degradation of sediment-derived DOM in macrophyte-dominated lakes was more intense under aerobic conditions. The microorganisms mainly metabolized the protein-like substances in the macrophyte-dominated lakes, and the carbohydrate-active enzyme genes and protein/lipid-like degradation genes played key roles in sediment-derived DOM degradation. Organic compounds with high H/C ratios such as lipids, carbohydrates, and protein/lipid-like compounds were preferentially removed by microorganisms during microbial degradation. Meanwhile, there was an increase in the abundance of organic molecular formula with a high aromaticity such as tannins and unsaturated hydrocarbons with low molecular weight and low double bond equivalent. In addition, aerobic/hypoxic environments can alter microbial metabolic pathways of sediment-derived DOM by affecting the relative abundance of microbial communities (e.g., Gemmatimonadetes and Acidobacteria) and functional genes (e.g., ABC.PE.P1 and ABC.PE.P) in macrophyte-dominated lakes. The abundances of lipids, unsaturated hydrocarbons, and protein compounds in aerobic environments decreased by 58 %, 50 %, and 44 %, respectively, compared to in hypoxic environments under microbial degradation. The results of this study deepen our understanding of DOM biodegradation in macrophyte-dominated lakes under different redox environments and provide new insights into nutrients releases from sediment and continuing eutrophication in macrophyte-dominated lakes.
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Affiliation(s)
- Wei Yu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; School of Resources and Environment, Anhui Agricultural University, Hefei 230036, PR China
| | - Haiquan Yang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China.
| | - Jingan Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Peng Liao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Jiaxi Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Lujia Jiang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; College of Biological and Environmental Engineering, Guiyang University, Guiyang 550005, PR China
| | - Wen Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
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4
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Zhang R, Liu P, Wang Y, Roberts AP, Bai J, Liu Y, Zhu K, Du Z, Chen G, Pan Y, Li J. Phylogenetics and biomineralization of a novel magnetotactic Gammaproteobacterium from a freshwater lake in Beijing, China. FEMS Microbiol Ecol 2023; 99:fiad150. [PMID: 37974050 DOI: 10.1093/femsec/fiad150] [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: 07/04/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023] Open
Abstract
Magnetotactic bacteria (MTB) have the remarkable capability of producing intracellularly membrane-enveloped magnetic nanocrystals (i.e. magnetosomes) and swimming along geomagnetic field lines. Despite more than 50 years of research, bacterial diversity and magnetosome biomineralization within MTB are relatively less known in the Gammaproteobacteria class than other groups. This is incompatible with the status of Gammaproteobacteria as the most diverse class of gram-negative bacteria with a number of ecologically important bacteria. Here, we identify a novel MTB strain YYHR-1 affiliated with the Gammaproteobacteria class of the Pseudomonadota phylum from a freshwater lake. In YYHR-1, most magnetosome crystals are organized into a long chain aligned along the cell long axis; unusually, a few small superparamagnetic crystals are located at the side of the chain, off the main chain axis. Micromagnetic simulations indicate that magnetostatic interactions among adjacent crystals within a chain reduce the Gibbs energy to enhance chain stability. Genomic analysis suggests that duplication of magnetosome gene clusters may result in off-chain magnetosomes formation. By integrating available genomic data from Gammaproteobacteria, the phylogenetic position of MTB in this class is reassigned here. Our new findings expand knowledge about MTB diversity and magnetosome biomineralization, and deepen understanding of the phylogenetics of the Gammaproteobacteria.
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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
- Marine College, Shandong University, Weihai 264209, 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 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
| | - Yuqin Wang
- 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
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - 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
- Marine College, Shandong University, Weihai 264209, 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
- 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
| | - Zongjun Du
- Marine College, Shandong University, Weihai 264209, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai 264209, China
| | - 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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5
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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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6
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Su Q, Bazylinski DA, Jensen MM. Effect of oxic and anoxic conditions on intracellular storage of polyhydroxyalkanoate and polyphosphate in Magnetospirillum magneticum strain AMB-1. Front Microbiol 2023; 14:1203805. [PMID: 37396362 PMCID: PMC10310966 DOI: 10.3389/fmicb.2023.1203805] [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: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms widely inhabiting the oxic-anoxic interface of aquatic environments. Beside biomineralizing magnetic nanocrystals, MTBs are able to sequester various chemical elements (e.g., carbon and phosphorus) for the biogenesis of intracellular granules, like polyhydroxyalkanoate (PHA) and polyphosphate (polyP), making them potentially important in biogeochemical cycling. Yet, the environmental controls of intracellular storage of carbon and phosphorus in MTB remain poorly understood. Here, we investigated the influence of oxic, anoxic and transient oxic-anoxic conditions on intracellular storage of PHA and polyP in Magnetospirillum magneticum strain AMB-1. In the incubations with oxygen, transmission electron microscopy revealed intercellular granules highly rich in carbon and phosphorus, which were further interpreted as PHA and polyP based on chemical and Energy-Dispersive X-ray spectroscopy analysis. Oxygen had a strong effect on PHA and polyP storage in AMB-1 cells, as PHA and polyP granules accounted for up to 47 ± 23% and 5.1 ± 1.7% of the cytoplasmic space, respectively, during continuous oxic conditions, while granules disappeared in anoxic incubations. Poly 3-hydroxybutyrate (PHB) and poly 3-hydroxyvalerate (PHV) accounted for 0.59 ± 0.66% and 0.0033 ± 0.0088% of dry cell weight, respectively, in anoxic incubations, while the values increased by a factor of 7 and 37 after oxygen was introduced. The results highlight a tight link between oxygen, carbon and phosphorus metabolisms in MTB, where favorable oxic growth conditions can lead to metabolic induction of polyP and PHA granule biogenesis.
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Affiliation(s)
- Qingxian Su
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Dennis A. Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, United States
| | - Marlene Mark Jensen
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
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7
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Zhao R, Babbin AR, Roerdink DL, Thorseth IH, Jørgensen SL. Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments. ISME COMMUNICATIONS 2023; 3:26. [PMID: 36991114 PMCID: PMC10060263 DOI: 10.1038/s43705-023-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Desiree L Roerdink
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Ingunn H Thorseth
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway.
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8
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Solhtalab M, Moller SR, Gu AZ, Jaisi D, Aristilde L. Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16441-16452. [PMID: 36283689 PMCID: PMC9670850 DOI: 10.1021/acs.est.2c04948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Among ubiquitous phosphorus (P) reserves in environmental matrices are ribonucleic acid (RNA) and polyphosphate (polyP), which are, respectively, organic and inorganic P-containing biopolymers. Relevant to P recycling from these biopolymers, much remains unknown about the kinetics and mechanisms of different acid phosphatases (APs) secreted by plants and soil microorganisms. Here we investigated RNA and polyP dephosphorylation by two common APs, a plant purple AP (PAP) from sweet potato and a fungal phytase from Aspergillus niger. Trends of δ18O values in released orthophosphate during each enzyme-catalyzed reaction in 18O-water implied a different extent of reactivity. Subsequent enzyme kinetics experiments revealed that A. niger phytase had 10-fold higher maximum rate for polyP dephosphorylation than the sweet potato PAP, whereas the sweet potato PAP dephosphorylated RNA at a 6-fold faster rate than A. niger phytase. Both enzymes had up to 3 orders of magnitude lower reactivity for RNA than for polyP. We determined a combined phosphodiesterase-monoesterase mechanism for RNA and terminal phosphatase mechanism for polyP using high-resolution mass spectrometry and 31P nuclear magnetic resonance, respectively. Molecular modeling with eight plant and fungal AP structures predicted substrate binding interactions consistent with the relative reactivity kinetics. Our findings implied a hierarchy in enzymatic P recycling from P-polymers by phosphatases from different biological origins, thereby influencing the relatively longer residence time of RNA versus polyP in environmental matrices. This research further sheds light on engineering strategies to enhance enzymatic recycling of biopolymer-derived P, in addition to advancing environmental predictions of this P recycling by plants and microorganisms.
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Affiliation(s)
- Mina Solhtalab
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Spencer R. Moller
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - April Z. Gu
- School
of Civil and Environmental Engineering, College of Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Deb Jaisi
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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9
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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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10
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Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications. NPJ Biofilms Microbiomes 2022; 8:43. [PMID: 35650214 PMCID: PMC9160268 DOI: 10.1038/s41522-022-00304-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 05/04/2022] [Indexed: 11/08/2022] Open
Abstract
Magnetotactic bacteria (MTB) are a group of phylogenetically diverse and morphologically varied microorganisms with a magnetoresponsive capability called magnetotaxis or microbial magnetoreception. MTB are a distinctive constituent of the microbiome of aquatic ecosystems because they use Earth's magnetic field to align themselves in a north or south facing direction and efficiently navigate to their favored microenvironments. They have been identified worldwide from diverse aquatic and waterlogged microbiomes, including freshwater, saline, brackish and marine ecosystems, and some extreme environments. MTB play important roles in the biogeochemical cycling of iron, sulphur, phosphorus, carbon and nitrogen in nature and have been recognized from in vitro cultures to sequester heavy metals like selenium, cadmium, and tellurium, which makes them prospective candidate organisms for aquatic pollution bioremediation. The role of MTB in environmental systems is not limited to their lifespan; after death, fossil magnetosomal magnetic nanoparticles (known as magnetofossils) are a promising proxy for recording paleoenvironmental change and geomagnetic field history. Here, we summarize the ecology, evolution, and environmental function of MTB and the paleoenvironmental implications of magnetofossils in light of recent discoveries.
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11
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Li J, Liu P, Menguy N, Zhang X, Wang J, Benzerara K, Feng L, Sun L, Zheng Y, Meng F, Gu L, Leroy E, Hao J, Chu X, Pan Y. Intracellular silicification by early-branching magnetotactic bacteria. SCIENCE ADVANCES 2022; 8:eabn6045. [PMID: 35559677 PMCID: PMC9106300 DOI: 10.1126/sciadv.abn6045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/31/2022] [Indexed: 06/13/2023]
Abstract
Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, 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
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, 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
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Xingliang Zhang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life and Environments and Department of Geology, Northwest University, Xi’an 710069, China
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, SK S7N 2V3, Canada
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Lianjun Feng
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Sun
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Fanqi Meng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lin Gu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Eric Leroy
- ICMPE, University Paris East, UMR 7182, CNRS, 2-8 Rue Henri Dunant, Thiais, Cedex 94320, France
| | - Jialong Hao
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuelei Chu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, 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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12
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Henkel JV, Schulz-Vogt HN, Dellwig O, Pollehne F, Schott T, Meeske C, Beier S, Jürgens K. Biological manganese-dependent sulfide oxidation impacts elemental gradients in redox-stratified systems: indications from the Black Sea water column. THE ISME JOURNAL 2022; 16:1523-1533. [PMID: 35124702 PMCID: PMC9122950 DOI: 10.1038/s41396-022-01200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/06/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
The reduction of manganese oxide with sulfide in aquatic redox-stratified systems was previously considered to be mainly chemical, but recent isolation of the Black Sea isolate Candidatus Sulfurimonas marisnigri strain SoZ1 suggests an important role for biological catalyzation. Here we provide evidence from laboratory experiments, field data, and modeling that the latter process has a strong impact on redox zonation in the Black Sea. High relative abundances of Sulfurimonas spp. across the redoxcline in the central western gyre of the Black Sea coincided with the high-level expression of both the sulfide:quinone oxidoreductase gene (sqr, up to 93% expressed by Sulfurimonas spp.) and other sulfur oxidation genes. The cell-specific rate of manganese-coupled sulfide oxidation by Ca. S. marisnigri SoZ1 determined experimentally was combined with the in situ abundance of Sulfurimonas spp. in a one-dimensional numerical model to calculate the vertical sulfide distribution. Abiotic sulfide oxidation was too slow to counterbalance the sulfide flux from euxinic water. We conclude that microbially catalyzed Mn-dependent sulfide oxidation influences the element cycles of Mn, S, C, and N and therefore the prevalence of other functional groups of prokaryotes (e.g., anammox bacteria) in a sulfide-free, anoxic redox zone.
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Affiliation(s)
- J V Henkel
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany.
| | - H N Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - O Dellwig
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - F Pollehne
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - T Schott
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - C Meeske
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - S Beier
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - K Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
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13
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Bidaud CC, Monteil CL, Menguy N, Busigny V, Jézéquel D, Viollier É, Travert C, Skouri-Panet F, Benzerara K, Lefevre CT, Duprat É. Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column. Front Microbiol 2022; 12:789134. [PMID: 35082768 PMCID: PMC8786505 DOI: 10.3389/fmicb.2021.789134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.
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Affiliation(s)
- Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France.,Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France.,Université de Paris, Centre de Recherches Interdisciplinaires (CRI), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Éric Viollier
- LSCE, CEA/CNRS/UVSQ/IPSL, Université Paris Saclay & Université de Paris France, Gif-sur-Yvette Cedex, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Élodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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14
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A Novel Magnetotactic Alphaproteobacterium Producing Intracellular Magnetite and Calcium-Bearing Minerals. Appl Environ Microbiol 2021; 87:e0155621. [PMID: 34756060 DOI: 10.1128/aem.01556-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that form intracellular magnetite (Fe3O4) or greigite (Fe3S4) nanocrystals with tailored sizes, often in chain configurations. Such magnetic particles are each surrounded by a lipid bilayer membrane, called a magnetosome, and provide a model system for studying the formation and function of specialized internal structures in prokaryotes. Using fluorescence-coupled scanning electron microscopy, we identified a novel magnetotactic spirillum, XQGS-1, from freshwater Xingqinggong Lake, Xi'an City, Shaanxi Province, China. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain XQGS-1 represents a novel genus of the Alphaproteobacteria class in the Proteobacteria phylum. Transmission electron microscopy analyses reveal that strain XQGS-1 forms on average 17 ± 3 magnetite magnetosome particles with an ideal truncated octahedral morphology, with an average length and width of 88.3 ± 11.7 nm and 83.3 ± 11.0 nm, respectively. They are tightly organized into a single chain along the cell long axis close to the concave side of the cell. Intrachain magnetic interactions likely result in these large equidimensional magnetite crystals behaving as magnetically stable single-domain particles that enable bacterial magnetotaxis. Combined structural and chemical analyses demonstrate that XQGS-1 cells also biomineralize intracellular amorphous calcium phosphate (2 to 3 granules per cell; 90.5- ± 19.3-nm average size) and weakly crystalline calcium carbonate (2 to 3 granules per cell; 100.4- ± 21.4-nm average size) in addition to magnetite. Our results expand the taxonomic diversity of MTB and provide evidence for intracellular calcium phosphate biomineralization in MTB. IMPORTANCE Biomineralization is a widespread process in eukaryotes that form shells, teeth, or bones. It also occurs commonly in prokaryotes, resulting in more than 60 known minerals formed by different bacteria under wide-ranging conditions. Among them, magnetotactic bacteria (MTB) are remarkable because they might represent the earliest organisms that biomineralize intracellular magnetic iron minerals (i.e., magnetite [Fe3O4] or greigite [Fe3S4]). Here, we report a novel magnetotactic spirillum (XQGS-1) that is phylogenetically affiliated with the Alphaproteobacteria class. In addition to magnetite crystals, XQGS-1 cells form intracellular submicrometer calcium carbonate and calcium phosphate granules. This finding supports the view that MTB are also an important microbial group for intracellular calcium carbonate and calcium phosphate biomineralization.
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15
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Fan X, Xing X, Ding S. Enhancing the retention of phosphorus through bacterial oxidation of iron or sulfide in the eutrophic sediments of Lake Taihu. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148039. [PMID: 34118662 DOI: 10.1016/j.scitotenv.2021.148039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Microbial activity can enhance the sequestration of phosphorus (P) in sediments, but little is known about the mechanisms behind it. In this study, sediment cores were sampled from the most eutrophic Meiliang Bay of Lake Taihu, and three treatments were set up in a laboratory incubation experiment, involving (a) the non-treated sediment cores, (b) inoculation, and (c) sterilization. The dissolved and labile iron (Fe) and P were obtained by high-resolution dialysis and the diffusive gradients in thin films (DGT) technique, respectively. AgI-based DGT was used for measuring the 2D distribution of labile sulfide. The bacterial community was investigated using a scanning electron microscope and 16S rRNA high throughput sequencing technique. The results showed that sterilization reduced the capacity of sediment to immobilize P, and that the critical sediment depth layer for microbial P sequestration was 0-10 mm. In addition, sterilization or inoculation significantly changes the structure of bacterial communities. Fe or S oxidation under micro-aerobic or anaerobic conditions played an important role in bacterial retention of P in the sediments. Nitrate-reducing coupling Fe(II)-oxidizing bacteria (Acidovorax) in the inoculated sediment and electrogenic sulfur-oxidizing bacteria (Candidatus Electronema) in the non-treated sediment were identified as the key bacterial genera responsible for the retention of P in sediments. This implies that bacterial communities could quickly establish the ability for negative feedback regulation by inoculation once the function and structure of indigenous sediment bacteria are seriously impaired, although this needs further validation in the field.
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Affiliation(s)
- Xianfang Fan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xigang Xing
- General Institute of Water Resources and Hydropower Planning and Design, Ministry of Water Resources, Beijing, China
| | - Shiming Ding
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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16
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Mandal FB. A review of the ecology, genetics, evolution, and magnetosome –induced behaviours of the magnetotactic bacteria. Isr J Ecol Evol 2021. [DOI: 10.1163/22244662-bja10028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The discovery of magnetosome and magnetotaxis in its most simple form in the magnetotactic bacteria (MTB) had created the tremendous impetus. MTB, spanning multiple phyla, are distributed worldwide, and they form the organelles called magnetosomes for biomineralization. Eight phylotypes of MTB belong to Alphaproteobacteria and Nitrospirae. MTB show preference for specific redox and oxygen concentration. Magnetosome chains function as the internal compass needle and align the bacterial cells passively along the local geomagnetic field (GMF). The nature of magnetosomes produced by MTB and their phylogeny suggest that bullet-shaped magnetites appeared about 3.2 billion years ago with the first magnetosomes. All MTB contains ten genes in conserved mamAB operon for magnetosome chain synthesis of which nine genes are conserved in greigite-producing MTB. Many candidate genes identify the aero-, redox-, and perhaps phototaxis. Among the prokaryotes, the MTB possess the highest number of O2-binding proteins. Magnetofossils serve as an indicator of oxygen and redox levels of the ancient environments. Most descendants of ancestral MTB lost the magnetosome genes in the course of evolution. Environmental conditions initially favored the evolution of MTB and expansion of magnetosome-formation genes. Subsequent changes in atmospheric oxygen concentration have led to changes in the ecology of MTB, loss of magnetosome genes, and evolution of nonMTB.
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Affiliation(s)
- Fatik Baran Mandal
- Department of Zoology, Bankura Christian College, College Road, Bankura, West Bengal, 722101, India
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17
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Melnikov V, Pollehne F, Minkina N, Melnik L. Distribution of Sprattus sprattus phalericus (Risso, 1827) and zooplankton near the Black Sea redoxcline. JOURNAL OF FISH BIOLOGY 2021; 99:1393-1402. [PMID: 34259352 DOI: 10.1111/jfb.14848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Understanding what environmental drivers influence marine predator-prey relationships can be key to managing and protecting ecosystems, especially in the face of future climate change risks. This is especially important in environments such as the Black Sea, where strong biogeochemical gradients can drive marine habitat partitioning and ecological interactions. We used underwater video recordings in the north-eastern Black Sea in November 2013 to observe the distribution and behaviour of the Black Sea sprat (Sprattus sprattus phalericus, Risso 1827) and its zooplankton prey. Video recordings have shown that the Black Sea sprat S. sprattus phalericus tolerates severely hypoxic waters near the redoxcline. The school was distributed in the 33-96 m layer [oxygen concentration (O2 ) 277-84 μmol L-1 ]. Some individuals were observed to leave the school and descended 20 m deeper for foraging on copepods in the 119-123 m layer (O2 12-10 μmol L-1 ). Zooplankton appeared concentrated on the upper boundary of the suboxic zone (O2 < 10 μmol L-1 ). No zooplankton were observed below O2 6-7 μmol L-1 (128 m). Understanding the ability of this species to tolerate low oxygen waters is crucial to predicting future responses to natural and anthropogenic changes in hypoxia.
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Affiliation(s)
- Victor Melnikov
- A. O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Falk Pollehne
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Natalia Minkina
- A. O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Lidia Melnik
- A. O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
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18
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Dixit R, Gupta A, Jordan N, Zhou S, Schild D, Weiss S, Guillon E, Jain R, Lens P. Magnetic properties of biogenic selenium nanomaterials. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40264-40274. [PMID: 33387313 DOI: 10.1007/s11356-020-11683-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Bioreduction of selenium oxyanions to elemental selenium is ubiquitous; elucidating the properties of this biogenic elemental selenium (BioSe) is thus important to understand its environmental fate. In this study, the magnetic properties of biogenic elemental selenium nanospheres (BioSe-Nanospheres) and nanorods (BioSe-Nanorods) obtained via the reduction of selenium(IV) using anaerobic granular sludge taken from an upflow anaerobic sludge blanket (UASB) reactor treating paper and pulp wastewater were investigated. The study indicated that the BioSe nanomaterials have a strong paramagnetic contribution with some ferromagnetic component due to the incorporation of Fe(III) (high-spin and low-spin species) as indicated by electron paramagnetic resonance (EPR). The paramagnetism did not saturate up to 50,000 Oe at 5 K, and the hysteresis curve showed the coercivity of 100 Oe and magnetic moment saturation around 10 emu. X-ray photoelectron spectroscopy (XPS) and EPR evidenced the presence of Fe(III) in the nanomaterial. Signals for Fe(II) were observed neither in EPR nor in XPS ruling out its presence in the BioSe nanoparticles. Fe(III) being abundantly present in the sludge likely got entrapped in the extracellular polymeric substances (EPS) coating the biogenic nanomaterials. The presence of Fe(III) in BioSe nanomaterial increases the mobility of Fe(III) and may have an effect on phytoplankton growth in the environment. Furthermore, as supported by the literature, there is a potential to exploit the magnetic properties of BioSe nanomaterials in drug delivery systems as well as in space refrigeration.
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Affiliation(s)
- Rewati Dixit
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New Delhi, 110016, India.
| | - Anirudh Gupta
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New Delhi, 110016, India
| | - Norbert Jordan
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328, Dresden, Germany
| | - Shengqiang Zhou
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Bautzner Landstrasse 400, 01328, Dresden, Germany
| | - Dieter Schild
- Institute for Nuclear Waste Disposal, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stephan Weiss
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328, Dresden, Germany
| | - Emmanuel Guillon
- Molecular Chemistry Institute of Reims (ICMR UMR CNRS 7312), Environmental Chemistry Group, University of Reims Chamapagne Ardenne, BP 1039, 51687 Reims cedex 2, France
| | - Rohan Jain
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New Delhi, 110016, India.
- Faculty of Engineering and Natural Sciences, Tampere University of Technology, P.O. Box 1001, FI-33014, Tampere, Finland.
| | - Piet Lens
- Faculty of Engineering and Natural Sciences, Tampere University of Technology, P.O. Box 1001, FI-33014, Tampere, Finland
- UNESCO-IHE, Westvest 7, 2611 AX, Delft, The Netherlands
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19
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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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20
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van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
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21
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Suominen S, Doorenspleet K, Sinninghe Damsté JS, Villanueva L. Microbial community development on model particles in the deep sulfidic waters of the Black Sea. Environ Microbiol 2021; 23:2729-2746. [PMID: 32291864 PMCID: PMC8359284 DOI: 10.1111/1462-2920.15024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/31/2022]
Abstract
Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
| | - Karlijn Doorenspleet
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
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22
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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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23
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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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24
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Inorganic Polyphosphate in Host and Microbe Biology. Trends Microbiol 2021; 29:1013-1023. [PMID: 33632603 DOI: 10.1016/j.tim.2021.02.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022]
Abstract
Inorganic polyphosphate (polyP) is produced by both bacteria and their eukaryotic hosts, and it appears to play multiple important roles in the interactions between those organisms. However, the detailed mechanisms of how polyP synthesis is regulated in bacteria, and how it influences both bacterial and host biology, remain largely unexplored. In this review, we examine recent developments in the understanding of how bacteria regulate the synthesis of polyP, what roles polyP plays in controlling virulence in pathogenic bacteria, and the effects of polyP on the mammalian immune system, as well as progress on developing drugs that may be able to target bacterial polyP synthesis as novel means of treating infectious disease.
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25
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Melnikov V, Melnik A, Mashukova O, Kapranov S, Melnik L. Bioluminescence of ctenophores near the boundary of oxygen-depleted waters at the redoxcline of the Black Sea. LUMINESCENCE 2021; 36:1063-1071. [PMID: 33600076 DOI: 10.1002/bio.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/05/2022]
Abstract
Vertical distribution of ctenophores near the boundary of oxygen-depleted waters of the Black Sea redoxcline was studied by use of video observations with real-time water sampling, horizontal MultiNet towing, and soundings using bathyphotometers with simultaneous vertical plankton net sampling. The results of the study showed for the first time that the daytime accumulation of ctenophores above the upper boundary of the suboxic zone changes the biophysical properties of the medium, causing an increase in the daytime intensity of bioluminescence near the redoxcline. The dynamics of this glow is in antiphase to that in the surface layers, where it is associated with the bioluminescence of phytoplankton. Therefore, in the deep-sea areas, two types of bioluminescence peaks differ in the light generation sources: the nighttime glow of phytoplankton in surface layers and the daytime glow of zooplankton in layers of oxygen-depleted waters at the redoxcline. The discovery of this new phenomenon allows the use of bioluminescent methods for the rapid assessment of the depth of the daytime zooplankton layers for the subsequent hauls of plankton nets. This significantly expands the possibilities of studying the structure and functioning of the pelagic ecosystem of the Black Sea and other marine basins with a redoxcline.
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Affiliation(s)
- Victor Melnikov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Russia
| | - Alexandr Melnik
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Russia
| | - Olga Mashukova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Russia
| | - Sergey Kapranov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Russia
| | - Lidia Melnik
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS), Russia
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26
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Henkel JV, Vogts A, Werner J, Neu TR, Spröer C, Bunk B, Schulz-Vogt HN. Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Syst Appl Microbiol 2020; 44:126155. [PMID: 33278714 DOI: 10.1016/j.syapm.2020.126155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL-1 (optimum 25gL-1). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL-1 (optimum 21gL-1). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H2), sulfide (H2S here taken as the sum of H2S, HS- and S2-), elemental sulfur (S0) and thiosulfate (S2O32-) as electron donors and nitrate (NO3-), oxygen (O2) and particulate manganese oxide (MnO2) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1T as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.
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Affiliation(s)
- Jan V Henkel
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany.
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Johannes Werner
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, 39114 Magdeburg, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Heide N Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
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27
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Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y. Expanding magnetic organelle biogenesis in the domain Bacteria. MICROBIOME 2020; 8:152. [PMID: 33126926 PMCID: PMC7602337 DOI: 10.1186/s40168-020-00931-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. RESULTS Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. CONCLUSIONS These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle. Video Abstract.
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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.
- Innovation Academy for 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
- Innovation Academy for 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 and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Greig A Paterson
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, L69 7ZE, Liverpool, UK
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92037, USA
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, ACT, Canberra, 2601, Australia
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
- Innovation Academy for 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 and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria. ISME JOURNAL 2020; 15:1-18. [PMID: 32839547 DOI: 10.1038/s41396-020-00747-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 11/08/2022]
Abstract
Bacteria synthesize a wide range of intracellular submicrometer-sized inorganic precipitates of diverse chemical compositions and structures, called biominerals. Their occurrences, functions and ultrastructures are not yet fully described despite great advances in our knowledge of microbial diversity. Here, we report bacteria inhabiting the sediments and water column of the permanently stratified ferruginous Lake Pavin, that have the peculiarity to biomineralize both intracellular magnetic particles and calcium carbonate granules. Based on an ultrastructural characterization using transmission electron microscopy (TEM) and synchrotron-based scanning transmission X-ray microscopy (STXM), we showed that the calcium carbonate granules are amorphous and contained within membrane-delimited vesicles. Single-cell sorting, correlative fluorescent in situ hybridization (FISH), scanning electron microscopy (SEM) and molecular typing of populations inhabiting sediments affiliated these bacteria to a new genus of the Alphaproteobacteria. The partially assembled genome sequence of a representative isolate revealed an atypical structure of the magnetosome gene cluster while geochemical analyses indicate that calcium carbonate production is an active process that costs energy to the cell to maintain an environment suitable for their formation. This discovery further expands the diversity of organisms capable of intracellular Ca-carbonate biomineralization. If the role of such biomineralization is still unclear, cell behaviour suggests that it may participate to cell motility in aquatic habitats as magnetite biomineralization does.
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29
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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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30
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Li J, Plouchart D, Zastepa A, Dittrich M. Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario. Sci Rep 2019; 9:19563. [PMID: 31862973 PMCID: PMC6925121 DOI: 10.1038/s41598-019-56042-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.
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Affiliation(s)
- Jiying Li
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada.
| | - Diane Plouchart
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Arthur Zastepa
- Canada Center for Inland Waters, Environment and Climate Change Canada, Burlington, ON, L7S 1A1, Canada
| | - Maria Dittrich
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
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31
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Koziaeva V, Dziuba M, Leão P, Uzun M, Krutkina M, Grouzdev D. Genome-Based Metabolic Reconstruction of a Novel Uncultivated Freshwater Magnetotactic coccus " Ca. Magnetaquicoccus inordinatus" UR-1, and Proposal of a Candidate Family " Ca. Magnetaquicoccaceae". Front Microbiol 2019; 10:2290. [PMID: 31632385 PMCID: PMC6783814 DOI: 10.3389/fmicb.2019.02290] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022] Open
Abstract
Magnetotactic bacteria are widely represented microorganisms that have the ability to synthesize magnetosomes. The magnetotactic cocci of the order Magnetococcales are the most frequently identified, but their classification remains unclear due to the low number of cultivated representatives. This paper reports the analysis of an uncultivated magnetotactic coccus UR-1 collected from the Uda River (in eastern Siberia). Genome analyses of this bacterium and comparison to the available Magnetococcales genomes identified a novel species called "Ca. Magnetaquicoccus inordinatus," and a delineated candidate family "Ca. Magnetaquicoccaceae" within the order Magnetococcales is proposed. We used average amino acid identity values <55-56% and <64-65% as thresholds for the separation of families and genera, respectively, within the order Magnetococcales. Analyses of the genome sequence of UR-1 revealed a potential ability for a chemolithoautotrophic lifestyle, with the oxidation of a reduced sulfur compound and carbon assimilation by rTCA. A nearly complete magnetosome genome island, containing a set of mam and mms genes, was also identified. Further comparative analyses of the magnetosome genes showed vertical inheritance as well as horizontal gene transfer as the evolutionary drivers of magnetosome biomineralization genes in strains of the order Magnetococcales.
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Affiliation(s)
- Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Marina Dziuba
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 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
| | - Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- 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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32
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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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33
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Abstract
Mn is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO2) as electron acceptor for the oxidation of organic compounds or hydrogen (H2), but so far the use of sulfide (H2S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO2 to the oxidation of H2S or thiosulfate (S2O32−) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H2S and S2O32− are oxidized completely to sulfate (SO42−) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO3]. In contrast to Mn-reducing bacteria, which use organic electron donors or H2, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.
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34
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Lin W, Kirschvink JL, Paterson GA, Bazylinski DA, Pan Y. On the origin of microbial magnetoreception. Natl Sci Rev 2019; 7:472-479. [PMID: 34692062 PMCID: PMC8288953 DOI: 10.1093/nsr/nwz065] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
A broad range of organisms, from prokaryotes to higher animals, have the ability to sense and utilize Earth's geomagnetic field—a behavior known as magnetoreception. Although our knowledge of the physiological mechanisms of magnetoreception has increased substantially over recent decades, the origin of this behavior remains a fundamental question in evolutionary biology. Despite this, there is growing evidence that magnetic iron mineral biosynthesis by prokaryotes may represent the earliest form of biogenic magnetic sensors on Earth. Here, we integrate new data from microbiology, geology and nanotechnology, and propose that initial biomineralization of intracellular iron nanoparticles in early life evolved as a mechanism for mitigating the toxicity of reactive oxygen species (ROS), as ultraviolet radiation and free-iron-generated ROS would have been a major environmental challenge for life on early Earth. This iron-based system could have later been co-opted as a magnetic sensor for magnetoreception in microorganisms, suggesting an origin of microbial magnetoreception as the result of the evolutionary process of exaptation.
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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
| | - Joseph L Kirschvink
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152–8551, Japan
| | - Greig A Paterson
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, 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 and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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