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Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK. Identification and cultivation of anaerobic bacterial scavengers of dead cells. THE ISME JOURNAL 2023; 17:2279-2289. [PMID: 37872273 PMCID: PMC10689501 DOI: 10.1038/s41396-023-01538-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
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Affiliation(s)
- Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
| | - Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Taiki Katayama
- Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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2
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Soares A, Edwards A, An D, Bagnoud A, Bradley J, Barnhart E, Bomberg M, Budwill K, Caffrey SM, Fields M, Gralnick J, Kadnikov V, Momper L, Osburn M, Mu A, Moreau JW, Moser D, Purkamo L, Rassner SM, Sheik CS, Sherwood Lollar B, Toner BM, Voordouw G, Wouters K, Mitchell AC. A global perspective on bacterial diversity in the terrestrial deep subsurface. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001172. [PMID: 36748549 PMCID: PMC9993121 DOI: 10.1099/mic.0.001172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/07/2022] [Indexed: 01/19/2023]
Abstract
While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
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Affiliation(s)
- A. Soares
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
- Present address: Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Campus Essen - Environmental Microbiology and Biotechnology, Universitätsstr. 5, 45141 Essen, Germany
| | - A. Edwards
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - D. An
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - A. Bagnoud
- Institut de Génie Thermique (IGT), Haute École d'Ingénierie et de Gestion du Canton de Vaud (HEIG-VD), Yverdon-les-Bains, Switzerland
| | - J. Bradley
- School of Geography, Queen Mary University of London, London, UK
| | - E. Barnhart
- U.S. Geological Survey (USGS), USA, Reston, VA, USA
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
| | - M. Bomberg
- VTT Technical Research Centre of Finland, Finland
| | | | | | - M. Fields
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
- Department of Microbiology & Immunology, MSU, Bozeman, MT, USA
| | - J. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | - V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Russia
| | - L. Momper
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), The Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - M. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - A. Mu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - J. W. Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Australia
| | - D. Moser
- Division of Hydrologic Sciences, Desert Research Institute (DRI), Las Vegas, NV, USA
| | - L. Purkamo
- VTT Technical Research Centre of Finland, Finland
- School of Earth and Environmental Sciences (SEES), University of St. Andrews, St. Andrews, UK
- Geological Survey of Finland (GTK), Finland
| | - S. M. Rassner
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - C. S. Sheik
- Large Lakes Observatory, University of Minnesota, Duluth, MN, USA
| | | | - B. M. Toner
- Department of Soil, Water & Climate, University of Minnesota, Minneapolis/Saint Paul, MN, USA
| | - G. Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - K. Wouters
- Institute for Environment, Health and Safety (EHS), Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - A. C. Mitchell
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
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3
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Nair S, Li C, Mou S, Zhang Z, Zhang Y. A Novel Phage Indirectly Regulates Diatom Growth by Infecting a Diatom-Associated Biofilm-Forming Bacterium. Appl Environ Microbiol 2022; 88:e0213821. [PMID: 35020448 PMCID: PMC8904054 DOI: 10.1128/aem.02138-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Algae and heterotrophic bacteria have close and intricate interactions, which are regulated by multiple factors in the natural environment. Phages are the major factor determining bacterial mortality rates. However, their impacts on the alga-associated bacteria and thus on the alga-bacterium interactions are poorly understood. Here, we obtained a diatom-associated bacterium, Stappia indica SNL01, that could form a biofilm and had an inhibitory effect on the growth of the diatom Thalassiosira pseudonana. Meanwhile, phage SI01, with a double-stranded circular DNA genome (44,247 bp), infecting S. indica SNL01 was isolated. Phylogenetic analysis revealed that phage SI01 represents a novel member of the Podoviridae family. The phage contained multiple lysis genes encoding cell wall-lysing muramidase and spore cortex-lysing SleB, as well as depolymerase-like tail spike protein. By lysing the host bacterium and inhibiting the formation of biofilm, this phage could indirectly promote the growth of the diatom. Our results provide new insights into how phages indirectly regulate algal growth by infecting bacteria that are closely associated with algae or in the phycosphere. IMPORTANCE The impact of phage infection on the alga-bacterium relationship in the ocean is poorly understood. Here, a novel phage infecting the diatom-associated bacterium Stappia indica SNL01 was isolated. This bacterium could form a biofilm and had a negative effect on diatom growth. We revealed that this phage contained multiple lysis genes and could inhibit the formation of the bacterial biofilm, thus indirectly promoting diatom growth. This study suggests that phages not only are important regulators of bacteria but also have substantial indirect effects on algae and the alga-bacterium relationship.
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Affiliation(s)
- Shailesh Nair
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanli Mou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Khomyakova MA, Merkel AY, Slobodkin AI. Perlabentimonas gracilis gen. nov., sp. nov., a gliding aerotolerant anaerobe of the order Bacteroidales, isolated from a terrestrial mud volcano. Syst Appl Microbiol 2021; 44:126245. [PMID: 34392063 DOI: 10.1016/j.syapm.2021.126245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/15/2022]
Abstract
A novel anaerobic bacterium (strain M08_MBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Gram-stain-negative cells were straight and slender rods with gliding motility, occasionally forming long filaments. The isolate was mesophilic, slightly halo- and alkaliphilic chemoorganoheterotroph, growing on carbohydrates (starch, dextrin, pectin, glucose, fructose, mannose, maltose, trehalose, lactose, sucrose) and proteinaceous compounds (peptone, tryptone, gelatin, casein and albumin). Strain M08_MBT tolerated 3% oxygen in the gas phase while catalase negative. The dominant cellular fatty acids of strain M08_MBT were C15:0, C15:1 and C13:0 acids. 16S rRNA gene sequence analysis revealed that strain M08_MBT belongs to the order Bacteroidales and only distantly related to other cultivated members of this order (85.12-90.01% 16S rRNA gene similarity). The genome of strain M08_MBT had a size of 4.37 Mb with a DNA G + C content of 43.5 mol% (WGS). The genes involved in gliding motility, proteolysis, central carbon metabolism, and oxygen tolerance were listed in genome annotation. Based on the phenotypic and genotypic characteristics, strain M08_MBT represents a novel species of a novel genus within family Tenuifilaceae, with proposed name Perlabentimonas gracilis gen. nov., sp. nov. The type strain is M08_ MBT (=DSM 110720 T = VKM B-3471 T). This is the first representative of Bacteroidales isolated in pure culture from a mud volcano.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
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5
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Gallardo-Carreño I, Moreno-Paz M, Aguirre J, Blanco Y, Alonso-Pintado E, Raymond-Bouchard I, Maggiori C, Rivas LA, Engelbrektson A, Whyte L, Parro V. A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration. Front Microbiol 2021; 11:590736. [PMID: 33391207 PMCID: PMC7772991 DOI: 10.3389/fmicb.2020.590736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Perchlorate anions are produced by chemical industries and are important contaminants in certain natural ecosystems. Perchlorate also occurs in some natural and uncontaminated environments such as the Atacama Desert, the high Arctic or the Antarctic Dry Valleys, and is especially abundant on the surface of Mars. As some bacterial strains are capable of using perchlorate as an electron acceptor under anaerobic conditions, their detection is relevant for environmental monitoring on Earth as well as for the search for life on Mars. We have developed an antibody microarray with 20 polyclonal antibodies to detect perchlorate-reducing bacteria (PRB) strains and two crucial and highly conserved enzymes involved in perchlorate respiration: perchlorate reductase and chlorite dismutase. We determined the cross-reactivity, the working concentration, and the limit of detection of each antibody individually and in a multiplex format by Fluorescent Sandwich Microarray Immunoassay. Although most of them exhibited relatively high sensitivity and specificity, we applied a deconvolution method based on graph theory to discriminate between specific signals and cross-reactions from related microorganisms. We validated the system by analyzing multiple bacterial isolates, crude extracts from contaminated reactors and salt-rich natural samples from the high Arctic. The PRB detecting chip (PRBCHIP) allowed us to detect and classify environmental isolates as well as to detect similar strains by using crude extracts obtained from 0.5 g even from soils with low organic-matter levels (<103 cells/g of soil). Our results demonstrated that PRBCHIP is a valuable tool for sensitive and reliable detection of perchlorate-reducing bacteria for research purposes, environmental monitoring and planetary exploration.
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Affiliation(s)
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain.,Centro Nacional de Biotecnología, CSIC, Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | | | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luis A Rivas
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain.,Inmunología y Genética Aplicada, S.A. (INGENASA), Madrid, Spain
| | - Anna Engelbrektson
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
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6
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Govil T, Sharma W, Chauhan NK, Kumar S, Salem DR, Sani RK. "MINES" method for genomic DNA extraction from deep biosphere biofilms. J Microbiol Methods 2019; 167:105730. [PMID: 31676422 DOI: 10.1016/j.mimet.2019.105730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 01/24/2023]
Abstract
Successful and efficient extraction of high quality, high molecular weight genomic DNA from the environmental samples is an essential primary step to understand the genetic, metabolic and evolutionary characteristics of the microbial communities. Deep mine biofilm samples that contain high amounts of mucoid exopolysaccharide often pose difficulties to obtaining refined community DNA. To circumvent this hindrance, we report our "MINES" method which we developed for optimal biofilm DNA recovery suitable for all types of high-resolution downstream applications. The method is also suitable for samples collected from landfill compost, kitchen digest (KD), and for Gram-positive Geobacillus sp. strain WSUCF1 and Gram-negative E. coli DH5α strains. In one form of the method, use of a gentle preprocessing technique to loosen the mucoid layer, combined with a multi-lytic polyzyme treatment to maximize yields from all cell types in the biofilm sample, yielded >1 μg of high molecular weight DNA (16-20 kb) per gram of the biofilm sample, with an A260/280 and A260/230 ratio of about 2. Furthermore, amplification of 16S rRNA genes as well as restriction digestion with BamHI and HindIII suggest that the newly developed method can minimize any inhibitory effects of contaminants. Results indicate that it is an appropriate methodology for the extraction of total genomic DNA for functional metagenomic studies and may be applicable to other environmental samples from which DNA extraction is challenging. IMPORTANCE: Our present knowledge of microorganisms and their enzymes from deep mine subsurfaces is based largely on laboratory studies of pure microbial cultures. These methods tend only to hit nearly 1% of the entire microbial community. In this regard, metagenomics, has emerged as a strategic approach to explore unculturable microbes through the sequencing and analysis of DNA extracted from the environmental samples. This research paper discusses our "MINES" method for genomic DNA extraction from deep biosphere biofilm samples.
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Affiliation(s)
- Tanvi Govil
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Wageesha Sharma
- Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Neeraj K Chauhan
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Sudhir Kumar
- Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - David R Salem
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; Composite and Nanocomposite Advanced Manufacturing Centre - Biomaterials (CNAM-Bio), Rapid City, SD 57701, USA; Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; Composites and Polymer Engineering Laboratory, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA.
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; Composite and Nanocomposite Advanced Manufacturing Centre - Biomaterials (CNAM-Bio), Rapid City, SD 57701, USA; BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA.
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Microbial Markers Profile in Anaerobic Mars Analogue Environments Using the LDChip (Life Detector Chip) Antibody Microarray Core of the SOLID (Signs of Life Detector) Platform. Microorganisms 2019; 7:microorganisms7090365. [PMID: 31540500 PMCID: PMC6780502 DOI: 10.3390/microorganisms7090365] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 09/16/2019] [Indexed: 11/30/2022] Open
Abstract
One of the main objectives for astrobiology is to unravel and explore the habitability of environments beyond Earth, paying special attention to Mars. If the combined environmental stress factors on Mars are compatible with life or if they were less harsh in the past, to investigate the traces of past or present life is critical to understand its potential habitability. Essential for this research is the characterization of Mars analogue environments on Earth through the development of techniques for biomarker detection in them. Biosensing techniques based on fluorescence sandwich microarray immunoassays (FSMI) have shown to be a powerful tool to detect biosignatures and depict the microbial profiles of different environments. In this study, we described the microbial biomarker profile of five anoxic Mars analogues sites using the Life Detector Chip (LDChip), an antibody microarray for multiple microbial marker detection. Furthermore, we contributed to new targets by developing a new 26-polyclonal antibodies microarray using crude extracts from anaerobic sampling sites, halophilic microorganisms, and anaerobic isolates obtained in the framework of the European Mars Analogues for Space Exploration (MASE) project. The new subset of antibodies was characterized and implemented into a microarray platform (MASE-Chip) for microbial marker searching in salty and anaerobic environments.
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8
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Parro V, Blanco Y, Puente-Sánchez F, Rivas LA, Moreno-Paz M, Echeverría A, Chong-Díaz G, Demergasso C, Cabrol NA. Biomarkers and Metabolic Patterns in the Sediments of Evolving Glacial Lakes as a Proxy for Planetary Lake Exploration. ASTROBIOLOGY 2018; 18:586-606. [PMID: 27893284 DOI: 10.1089/ast.2015.1342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Oligotrophic glacial lakes in the Andes Mountains serve as models to study the effects of climate change on natural biological systems. The persistent high UV regime and evolution of the lake biota due to deglaciation make Andean lake ecosystems potential analogues in the search for life on other planetary bodies. Our objective was to identify microbial biomarkers and metabolic patterns that represent time points in the evolutionary history of Andean glacial lakes, as these may be used in long-term studies as microscale indicators of climate change processes. We investigated a variety of microbial markers in shallow sediments from Laguna Negra and Lo Encañado lakes (Región Metropolitana, Chile). An on-site immunoassay-based Life Detector Chip (LDChip) revealed the presence of sulfate-reducing bacteria, methanogenic archaea, and exopolymeric substances from Gammaproteobacteria. Bacterial and archaeal 16S rRNA gene sequences obtained from field samples confirmed the results from the immunoassays and also revealed the presence of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, as well as cyanobacteria and methanogenic archaea. The complementary immunoassay and phylogenetic results indicate a rich microbial diversity with active sulfate reduction and methanogenic activities along the shoreline and in shallow sediments. Sulfate inputs from the surrounding volcanic terrains during deglaciation may explain the observed microbial biomarker and metabolic patterns, which differ with depth and between the two lakes. A switch from aerobic and heterotrophic metabolisms to anaerobic ones such as sulfate reduction and methanogenesis in the shallow shores likely reflects the natural evolution of the lake sediments due to deglaciation. Hydrodynamic deposition of sediments creates compartmentalization (e.g., sediments with different structure and composition surrounded by oligotrophic water) that favors metabolic transitions. Similar phenomena would be expected to occur on other planetary lakes, such as those of Titan, where watery niches fed by depositional events would be surrounded by a "sea" of hydrocarbons. Key Words: Glacier lakes-Sedimentation-Prokaryotic metabolisms and biomarkers-Deglaciation-Life detection-Planetary exploration. Astrobiology 18, 586-606.
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Affiliation(s)
- Víctor Parro
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Yolanda Blanco
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | | | - Luis A Rivas
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Mercedes Moreno-Paz
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Alex Echeverría
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Guillermo Chong-Díaz
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Cecilia Demergasso
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Nathalie A Cabrol
- 3 The SETI Institute , Carl Sagan Center, Mountain View, California, and NASA Ames Research Center, Moffett Field, California, USA
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9
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Schuelke T, Pereira TJ, Hardy SM, Bik HM. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol Ecol 2018; 27:1930-1951. [DOI: 10.1111/mec.14539] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Taruna Schuelke
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Tiago José Pereira
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Sarah M. Hardy
- School of Fisheries and Ocean Sciences; University of Alaska; Fairbanks AK USA
| | - Holly M. Bik
- Department of Nematology; University of California, Riverside; Riverside CA USA
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10
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Blanco Y, Gallardo-Carreño I, Ruiz-Bermejo M, Puente-Sánchez F, Cavalcante-Silva E, Quesada A, Prieto-Ballesteros O, Parro V. Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario. ASTROBIOLOGY 2017; 17:984-996. [PMID: 29016195 PMCID: PMC5655591 DOI: 10.1089/ast.2016.1467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/20/2017] [Indexed: 05/17/2023]
Abstract
The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration-Life detection-Microbial mat-Life detector chip-Thermogravimetry-Raman spectroscopy-NIR-DRIFTS. Astrobiology 17, 984-996.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | - Marta Ruiz-Bermejo
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | | | - Antonio Quesada
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
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11
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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12
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Blanco Y, Moreno-Paz M, Parro V. Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip. J Vis Exp 2017. [PMID: 28287562 DOI: 10.3791/54994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Global warming and eutrophication make some aquatic ecosystems behave as true bioreactors that trigger rapid and massive cyanobacterial growth; this has relevant health and economic consequences. Many cyanobacterial strains are toxin producers, and only a few cells are necessary to induce irreparable damage to the environment. Therefore, water-body authorities and administrations require rapid and efficient early-warning systems providing reliable data to support their preventive or curative decisions. This manuscript reports an experimental protocol for the in-field detection of toxin-producing cyanobacterial strains by using an antibody microarray chip with 17 antibodies (Abs) with taxonomic resolution (CYANOCHIP). Here, a multiplex fluorescent sandwich microarray immunoassay (FSMI) for the simultaneous monitoring of 17 cyanobacterial strains frequently found blooming in freshwater ecosystems, some of them toxin producers, is described. A microarray with multiple identical replicates (up to 24) of the CYANOCHIP was printed onto a single microscope slide to simultaneously test a similar number of samples. Liquid samples can be tested either by direct incubation with the antibodies (Abs) or after cell concentration by filtration through a 1- to 3-μm filter. Solid samples, such as sediments and ground rocks, are first homogenized and dispersed by a hand-held ultrasonicator in an incubation buffer. They are then filtered (5 - 20 μm) to remove the coarse material, and the filtrate is incubated with Abs. Immunoreactions are revealed by a final incubation with a mixture of the 17 fluorescence-labeled Abs and are read by a portable fluorescence detector. The whole process takes around 3 h, most of it corresponding to two 1-h periods of incubation. The output is an image, where bright spots correspond to the positive detection of cyanobacterial markers.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CAB, INTA-CSIC)
| | | | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB, INTA-CSIC);
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13
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Brazelton WJ, Thornton CN, Hyer A, Twing KI, Longino AA, Lang SQ, Lilley MD, Früh-Green GL, Schrenk MO. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ 2017; 5:e2945. [PMID: 28149702 PMCID: PMC5274519 DOI: 10.7717/peerj.2945] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/27/2016] [Indexed: 12/22/2022] Open
Abstract
The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
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Affiliation(s)
- William J Brazelton
- Department of Biology, University of Utah , Salt Lake City , UT , United States
| | | | - Alex Hyer
- Department of Biology, University of Utah , Salt Lake City , UT , United States
| | - Katrina I Twing
- Department of Earth and Environmental Sciences, Michigan State University , East Lansing , MI , United States
| | - August A Longino
- Department of Biology, University of Utah , Salt Lake City , UT , United States
| | - Susan Q Lang
- Department of Earth and Ocean Sciences, University of South Carolina, Columbia, SC, United States; Department of Earth Sciences, ETH Zurich, Zurich, Switzerland
| | - Marvin D Lilley
- School of Oceanography, University of Washington , Seattle , WA , United States
| | | | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University , East Lansing , MI , United States
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Podosokorskaya OA, Merkel AY, Gavrilov SN, Fedoseev I, Heerden EV, Cason ED, Novikov AA, Kolganova TV, Korzhenkov AA, Bonch-Osmolovskaya EA, Kublanov IV. Tepidibacillus infernus sp. nov., a moderately thermophilic, selenate- and arsenate-respiring hydrolytic bacterium isolated from a gold mine, and emended description of the genus Tepidibacillus. Int J Syst Evol Microbiol 2016; 66:3189-3194. [DOI: 10.1099/ijsem.0.001166] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Olga A. Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Igor Fedoseev
- Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Esta van Heerden
- TIA-UFS SAENSE Platform, University of the Free State, Bloemfontein, South Africa
| | - Errol D. Cason
- TIA-UFS SAENSE Platform, University of the Free State, Bloemfontein, South Africa
| | | | - Tatyana V. Kolganova
- Bioengineering Center, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Blanco Y, Quesada A, Gallardo-Carreño I, Aguirre J, Parro V. CYANOCHIP: an antibody microarray for high-taxonomical-resolution cyanobacterial monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1611-1620. [PMID: 25565212 DOI: 10.1021/es5051106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cyanobacteria are Gram-negative photosynthetic prokaryotes that are widespread on Earth. Eutrophication and global warming make some aquatic ecosystems behave as bioreactors that trigger rapid and massive cyanobacterial growth with remarkable economic and health consequences. Rapid and efficient early warning systems are required to support decisions by water body authorities. We have produced 17 specific antibodies to the most frequent cyanobacterial strains blooming in freshwater ecosystems, some of which are toxin producers. A sandwich-type antibody microarray immunoassay (CYANOCHIP) was developed for the simultaneous testing of any of the 17 strains, or other closely related strains, in field samples from different habitats (water, rocks, and sediments). We titrated and tested all of the antibodies in succession using a fluorescent sandwich microarray immunoassay. Although most showed high specificity, we applied a deconvolution method based on graph theory to disentangle the few existing cross-reactions. The CYANOCHIP sensitivity ranged from 10(2) to 10(4) cells mL(-1), with most antibodies detecting approximately 10(2) cells mL(-1). We validated the system by testing multiple isolates and crude natural samples from freshwater reservoirs and rocks, both in the laboratory and by in situ testing in the field. The results demonstrated that CYANOCHIP is a valuable tool for the sensitive and reliable detection of cyanobacteria for early warning and research purposes.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
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