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Karthik P, Jose PA, Chellakannu A, Gurusamy S, Ananthappan P, Karuppathevan R, Vasantha VS, Rajesh J, Ravichandran S, Sankarganesh M. Green synthesis of MnO 2 nanoparticles from Psidium guajava leaf extract: Morphological characterization, photocatalytic and DNA/BSA interaction studies. Int J Biol Macromol 2024; 258:128869. [PMID: 38114013 DOI: 10.1016/j.ijbiomac.2023.128869] [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: 08/02/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
In this work, a simple, efficient and eco-friendly green synthesis of manganese dioxide nanoparticles (MnO2NPs) by Psidium guajava leaf extract was described. Fourier-Transform infrared spectra results revealed that involvement of the plant extract functional groups in the formation of MnO2NPs. The UV-vis absorption spectra of the synthesized MnO2NPs exhibited absorption peaks at 374 nm, which were attributed to the band gap of the MnO2NPs. Crystal phase identification of the MnO2NPs were characterized by X-ray diffraction analysis and the formation of crystalline MnO2NPs have been confirmed. Furthermore, scanning electron microscopy analysis showed that the synthesized MnO2NPs have a spherical in shape. Interestingly, the prepared green synthesized MnO2NPs showed catalytic degradation activity for malachite green dye. Malachite green's photocatalytic degradation was detected spectrophotometrically in the wavelength range of 250-900 nm, and it was discovered to have a photodegradation efficiency of 75.5 % within 90 min when exposed to solar radiation. Green synthesized MnO2NPs are responsible for this higher activity. An interaction between synthesized NPs and biomolecules, including CT-DNA and BSA was also evaluated. The spectrophotometric and Fluoro spectroscopic analyses indicate a gradual reduction in peak intensities and shifts in wavelengths, indicating binding and affinity between the NPs and the biomolecules.
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Affiliation(s)
- Palani Karthik
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105, India
| | - Paulraj Adwin Jose
- Department of Science and Humanities (Chemistry), E.G.S. Pillay Engineering College, Nagapattinam, Tamil Nadu 611 002, India
| | - Arunbalaji Chellakannu
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021, India
| | | | - Periyasamy Ananthappan
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021, India
| | - Ramki Karuppathevan
- Department of Immunology, School of Biological Science, Madurai Kamaraj University, Madurai, Tamil Nadu 625021, India
| | - Vairathevar Sivasamy Vasantha
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021, India
| | - Jegathalaprathaban Rajesh
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105, India.
| | - Siranjeevi Ravichandran
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105, India
| | - Murugesan Sankarganesh
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105, India.
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Koito T, Ito Y, Suzuki A, Tame A, Ikuta T, Suzuki M, Mitsunobu S, Sugimura M, Inoue K. Difference in sulfur regulation mechanism between tube-dwelling and free-moving polychaetes sympatrically inhabiting deep-sea hydrothermal chimneys. ZOOLOGICAL LETTERS 2023; 9:18. [PMID: 37789380 PMCID: PMC10548688 DOI: 10.1186/s40851-023-00218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/03/2023] [Indexed: 10/05/2023]
Abstract
The environment around deep sea hydrothermal vents is characterized by an abundance of sulfur compounds, including toxic hydrogen sulfide. However, numerous communities of various invertebrates are found in it. It is suggested that invertebrates in the vicinity of hydrothermal vents detoxify sulfur compounds by biosynthesis of taurine-related compounds in the body. On the other hand, the vent endemic polychaete Alvinella pompejana has spherocrystals composed of sulfur and other metals in its digestive tract. It was considered that the spherocrystals contribute to the regulation of sulfur in body fluids. Paralvinella spp. and Polynoidae. gen. sp. live sympatrically and in areas most affected by vent fluid. In this study, we focused on the digestive tract of Paralvinella spp. and Polynoidae. gen. sp. to examine whether they have spherocrystals. We also investigated the possible involvement of bacteria in the digestive tract in spherulization. Examination with a scanning electron microscope (SEM) equipped with Energy Disperse X-ray Spectroscopy (EDS) detected spherocrystals containing sulfur and iron in the digestive tract of Paralvinella spp. In contrast, such spherocrystals were not observed in that of Polynoidae. gen. sp. although sulfur is detected there by inductively coupled plasma-optical emission spectrometry (ICP-OES). Meta-16S rRNA analysis indicated that the floras of the digestive tracts of the two species were very similar, suggesting that enteric bacteria are not responsible for spherocrystal formation. Analysis of taurine-related compounds indicated that the digestive tissues of Polynoidae. gen. sp. contain a higher amount of hypotaurine and thiotaurine than those of Paralvinella spp. Therefore, the two sympatric polychaetes use different strategies for controlling sulfur, i.e., Paralvinella spp. forms spherocrystals containing elemental sulfur and iron in the digestive tract, but Polynoidae. gen. sp. accumulates taurine-related compounds instead of spherocrystals. Such differences may be related to differences in their lifestyles, i.e., burrow-dweller or free-moving, or may have been acquired phylogenetically in the evolutionary process.
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Affiliation(s)
- Tomoko Koito
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Yusuke Ito
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Akihiko Suzuki
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
- Present Address: National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Akihiro Tame
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka, Kanagawa, 237-0063, Japan
| | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Miwa Suzuki
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Satoshi Mitsunobu
- Department of Science and Technology for Biological Resources and Environment, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Makoto Sugimura
- Enoshima Aquarium, 2-19-1 Katase, Fujisawa, Kanagawa, 251-0035, Japan
| | - Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-Shi, Chiba, 277-8564, Japan
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3
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Gao ZM, Xu T, Chen HG, Lu R, Tao J, Wang HB, Qiu JW, Wang Y. Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm. iScience 2023; 26:107033. [PMID: 37389180 PMCID: PMC10300362 DOI: 10.1016/j.isci.2023.107033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/11/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Endosymbiosis with chemosynthetic Gammaproteobacteria is widely recognized as an adaptive mechanism of siboglinid tubeworms, yet evolution of these endosymbionts and their driving forces remain elusive. Here, we report a finished endosymbiont genome (HMS1) of the cold-seep tubeworm Sclerolinum annulatum. The HMS1 genome is small in size, with abundant prophages and transposable elements but lacking gene sets coding for denitrification, hydrogen oxidization, oxidative phosphorylation, vitamin biosynthesis, cell pH and/or sodium homeostasis, environmental sensing, and motility, indicative of early genome erosion and adaptive evolution toward obligate endosymbiosis. Unexpectedly, a prophage embedded in the HMS1 genome undergoes lytic cycle. Highly expressed ROS scavenger and LexA repressor genes indicate that the tubeworm host likely activates the lysogenic phage into lytic cycle through the SOS response to regulate endosymbiont population and harvest nutrients. Our findings indicate progressive evolution of Sclerolinum endosymbionts toward obligate endosymbiosis and expand the knowledge about phage-symbiont-host interaction in deep-sea tubeworms.
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Affiliation(s)
- Zhao-Ming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
| | - Ting Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hua-Guan Chen
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Lu
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Hong-Bin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518000, China
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4
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He W, Cai R, Xi S, Yin Z, Du Z, Luan Z, Sun C, Zhang X. Study of Microbial Sulfur Metabolism in a Near Real-Time Pathway through Confocal Raman Quantitative 3D Imaging. Microbiol Spectr 2023; 11:e0367822. [PMID: 36809047 PMCID: PMC10101092 DOI: 10.1128/spectrum.03678-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
As microbial sulfur metabolism significantly contributes to the formation and cycling of deep-sea sulfur, studying their sulfur metabolism is important for understanding the deep-sea sulfur cycle. However, conventional methods are limited in near real-time studies of bacterial metabolism. Recently, Raman spectroscopy has been widely used in studies on biological metabolism due to its low-cost, rapid, label-free, and nondestructive features, providing us with new approaches to solve the above limitation. Here, we used the confocal Raman quantitative 3D imaging method to nondestructively detect the growth and metabolism of Erythrobacter flavus 21-3 in the long term and near real time, which possessed a pathway mediating the formation of elemental sulfur in the deep sea, but the dynamic process was unknown. In this study, its dynamic sulfur metabolism was visualized and quantitatively assessed in near real time using 3D imaging and related calculations. Based on 3D imaging, the growth and metabolism of microbial colonies growing under both hyperoxic and hypoxic conditions were quantified by volume calculation and ratio analysis. Additionally, unprecedented details of growth and metabolism were uncovered by this method. Due to this successful application, this method is potentially significant for analyzing the in situ biological processes of microorganisms in the future. IMPORTANCE Microorganisms contribute significantly to the formation of deep-sea elemental sulfur, so studies on their growth and dynamic sulfur metabolism are important to understand the deep-sea sulfur cycle. However, near real-time in situ nondestructive metabolic studies of microorganisms remain a great challenge due to the limitations of existing methods. We thus used an imaging-related workflow by confocal Raman microscopy. More detailed descriptions of the sulfur metabolism of E. flavus 21-3 were disclosed, which perfectly complemented previous research results. Therefore, this method is potentially significant for analyzing the in-situ biological processes of microorganisms in the future. To our knowledge, this is the first label-free and nondestructive in situ technique that can provide temporally persistent 3D visualization and quantitative information about bacteria.
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Affiliation(s)
- Wanying He
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ruining Cai
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shichuan Xi
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Ziyu Yin
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zengfeng Du
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhendong Luan
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xin Zhang
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
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5
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Deep-Sea
In Situ
Insights into the Formation of Zero-Valent Sulfur Driven by a Bacterial Thiosulfate Oxidation Pathway. mBio 2022; 13:e0014322. [PMID: 35852328 PMCID: PMC9426585 DOI: 10.1128/mbio.00143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The contribution of microbes to the deep-sea cold seep sulfur cycle has received considerable attention in recent years. In the previous study, we isolated
E. flavus
21-3 from deep-sea cold seep sediments and described a novel thiosulfate oxidation pathway in the laboratorial condition.
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6
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Nazeer Z, Fernando EY. A novel growth and isolation medium for exoelectrogenic bacteria. Enzyme Microb Technol 2022; 155:109995. [DOI: 10.1016/j.enzmictec.2022.109995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 01/16/2023]
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7
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Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
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8
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Rincón-Tomás B, González FJ, Somoza L, Sauter K, Madureira P, Medialdea T, Carlsson J, Reitner J, Hoppert M. Siboglinidae Tubes as an Additional Niche for Microbial Communities in the Gulf of Cádiz-A Microscopical Appraisal. Microorganisms 2020; 8:E367. [PMID: 32150959 PMCID: PMC7143560 DOI: 10.3390/microorganisms8030367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/24/2020] [Accepted: 02/29/2020] [Indexed: 11/30/2022] Open
Abstract
Siboglinids were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV, and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in a dedicated trophosome organ. However, little is known about their tube as a potential niche for other microorganisms. Analyses by scanning and transmission electron microscopy showed dense biofilms on the tube in Al Gacel MV and Anastasya MV specimens by prokaryotic cells. Methanotrophic bacteria were the most abundant forming these biofilms as further supported by 16S rRNA sequence analysis. Furthermore, elemental analyses with electron microscopy and energy-dispersive X-ray spectroscopy point to the mineralization and silicification of the tube, most likely induced by the microbial metabolisms. Bacterial and archaeal 16S rRNA sequence libraries revealed abundant microorganisms related to these siboglinid specimens and certain variations in microbial communities among samples. Thus, the tube remarkably increases the microbial biomass related to the worms and provides an additional microbial niche in deep-sea ecosystems.
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Affiliation(s)
- Blanca Rincón-Tomás
- Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany; (K.S.); (M.H.)
- Göttingen Centre of Geosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany;
| | | | - Luis Somoza
- Marine Geology Dv., Geological Survey of Spain, IGME, 28003 Madrid, Spain; (F.J.G.); (L.S.); (T.M.)
| | - Kathrin Sauter
- Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany; (K.S.); (M.H.)
| | - Pedro Madureira
- Estrutura de Missão para a Extensão da Plataforma Continental (EMEPC), 2770-047 Paço de Arcos, Portugal;
| | - Teresa Medialdea
- Marine Geology Dv., Geological Survey of Spain, IGME, 28003 Madrid, Spain; (F.J.G.); (L.S.); (T.M.)
| | - Jens Carlsson
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, University College Dublin, Dublin 4, Ireland;
| | - Joachim Reitner
- Göttingen Centre of Geosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany;
- Göttingen Academy of Sciences and Humanities, 37073 Göttingen, Germany
| | - Michael Hoppert
- Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany; (K.S.); (M.H.)
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9
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Bacterial Intracellular Sulphur Globules. BACTERIAL ORGANELLES AND ORGANELLE-LIKE INCLUSIONS 2020. [DOI: 10.1007/978-3-030-60173-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Low frequency Raman Spectroscopy for micron-scale and in vivo characterization of elemental sulfur in microbial samples. Sci Rep 2019; 9:7971. [PMID: 31138888 PMCID: PMC6538736 DOI: 10.1038/s41598-019-44353-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
Elemental sulfur (S(0)) is an important intermediate of the sulfur cycle and is generated by chemical and biological sulfide oxidation. Raman spectromicroscopy can be applied to environmental samples for the detection of S(0), as a practical non-destructive micron-scale method for use on wet material and living cells. Technical advances in filter materials enable the acquisition of ultra-low frequency (ULF) Raman measurements in the 10–100 cm−1 range using a single-stage spectrometer. Here we demonstrate the potency of ULF Raman spectromicroscopy to harness the external vibrational modes of previously unrecognized S(0) structures present in environmental samples. We investigate the chemical and structural nature of intracellular S(0) granules stored within environmental mats of sulfur-oxidizing γ-Proteobacteria (Thiothrix). In vivo intracellular ULF scans indicate the presence of amorphous cyclooctasulfur (S8), clarifying enduring uncertainties regarding the content of microbial sulfur storage globules. Raman scattering of extracellular sulfur clusters in Thiothrix mats furthermore reveals an unexpected abundance of metastable β-S8 and γ-S8, in addition to the stable α-S8 allotrope. We propose ULF Raman spectroscopy as a powerful method for the micron-scale determination of S(0) structure in natural and laboratory systems, with a promising potential to shine new light on environmental microbial and chemical sulfur cycling mechanisms.
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11
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Gill S, Catchpole R, Forterre P. Extracellular membrane vesicles in the three domains of life and beyond. FEMS Microbiol Rev 2019; 43:273-303. [PMID: 30476045 PMCID: PMC6524685 DOI: 10.1093/femsre/fuy042] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.
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Affiliation(s)
- Sukhvinder Gill
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
| | - Ryan Catchpole
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
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Hydrocarbonoclastic Ascomycetes to enhance co-composting of total petroleum hydrocarbon (TPH) contaminated dredged sediments and lignocellulosic matrices. N Biotechnol 2019; 50:27-36. [PMID: 30654133 DOI: 10.1016/j.nbt.2019.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 02/06/2023]
Abstract
Four new Ascomycete fungi capable of degrading diesel oil were isolated from sediments of a river estuary mainly contaminated by shipyard fuels or diesel oil. The isolates were identified as species of Lambertella, Penicillium, Clonostachys, and Mucor. The fungal candidates degraded and adsorbed the diesel oil in suspension cultures. The Lambertella sp. isolate displayed the highest percentages of oxidation of diesel oil and was characterised by the capacity to utilise the latter as a sole carbon source. This isolate showed extracellular laccase and Mn-peroxidase activities in the presence of diesel oil. It was tested for capacity to accelerate the process of decontamination of total petroleum hydrocarbon contaminated sediments, co-composted with lignocellulosic residues and was able to promote the degradation of 47.6% of the TPH contamination (54,074 ± 321 mg TPH/Kg of sediment) after two months of incubation. The response of the bacterial community during the degradation process was analysed by 16S rRNA gene meta-barcoding.
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13
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Evolution of Sulfur Binding by Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone-Eating Worms, Osedax. J Mol Evol 2016; 82:219-29. [PMID: 27100359 DOI: 10.1007/s00239-016-9739-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
Most members of Siboglinidae (Annelida) harbor endosymbiotic bacteria that allow them to thrive in extreme environments such as hydrothermal vents, methane seeps, and whale bones. These symbioses are enabled by specialized hemoglobins (Hbs) that are able to bind hydrogen sulfide for transportation to their chemosynthetic endosymbionts. Sulfur-binding capabilities are hypothesized to be due to cysteine residues at key positions in both vascular and coelomic Hbs, especially in the A2 and B2 chains. Members of the genus Osedax, which live on whale bones, do not have chemosynthetic endosymbionts, but instead harbor heterotrophic bacteria capable of breaking down complex organic compounds. Although sulfur-binding capabilities are important in other siboglinids, we questioned whether Osedax retained these cysteine residues and the potential ability to bind hydrogen sulfide. To answer these questions, we used high-throughput DNA sequencing to isolate and analyze Hb sequences from 8 siboglinid lineages. For Osedax mucofloris, we recovered three (A1, A2, and B1) Hb chains, but the B2 chain was not identified. Hb sequences from gene subfamilies A2 and B2 were translated and aligned to determine conservation of cysteine residues at previously identified key positions. Hb linker sequences were also compared to determine similarity between Osedax and siboglinids/sulfur-tolerant annelids. For O. mucofloris, our results found conserved cysteines within the Hb A2 chain. This finding suggests that Hb in O. mucofloris has retained some capacity to bind hydrogen sulfide, likely due to the need to detoxify this chemical compound that is abundantly produced within whale bones.
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Sulfur vesicles from Thermococcales: A possible role in sulfur detoxifying mechanisms. Biochimie 2015; 118:356-64. [PMID: 26234734 PMCID: PMC4640147 DOI: 10.1016/j.biochi.2015.07.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/28/2015] [Indexed: 11/21/2022]
Abstract
The euryarchaeon Thermococcus prieurii inhabits deep-sea hydrothermal vents, one of the most extreme environments on Earth, which is reduced and enriched with heavy metals. Transmission electron microscopy and cryo-electron microscopy imaging of T. prieurii revealed the production of a plethora of diverse membrane vesicles (MVs) (from 50 nm to 400 nm), as is the case for other Thermococcales. T. prieurii also produces particularly long nanopods/nanotubes, some of them containing more than 35 vesicles encased in a S-layer coat. Notably, cryo-electron microscopy of T. prieurii cells revealed the presence of numerous intracellular dark vesicles that bud from the host cells via interaction with the cytoplasmic membrane. These dark vesicles are exclusively found in conjunction with T. prieurii cells and never observed in the purified membrane vesicles preparations. Energy-Dispersive-X-Ray analyses revealed that these dark vesicles are filled with sulfur. Furthermore, the presence of these sulfur vesicles (SVs) is exclusively observed when elemental sulfur was added into the growth medium. In this report, we suggest that these atypical vesicles sequester the excess sulfur not used for growth, thus preventing the accumulation of toxic levels of sulfur in the host's cytoplasm. These SVs transport elemental sulfur out of the cell where they are rapidly degraded. Intriguingly, closely related archaeal species, Thermococcus nautili and Thermococcus kodakaraensis, show some differences about the production of sulfur vesicles. Whereas T. kodakaraensis produces less sulfur vesicles than T. prieurii, T. nautili does not produce such sulfur vesicles, suggesting that Thermococcales species exhibit significant differences in their sulfur metabolic pathways.
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