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Wang C, Hou L, Jiang N, Wang Y, Mao X, Zhou P, Xia Y, Wang Y, Chen C, Yang X, Luo Q, Pan J. Microbial diversity in earthen site of exhibition Hall of pit no. 1 at the terracotta warriors Museum in Emperor Qinshihuang's mausoleum site museum and its correlation with environmental factors. Front Microbiol 2024; 15:1378180. [PMID: 39372268 PMCID: PMC11449754 DOI: 10.3389/fmicb.2024.1378180] [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: 01/29/2024] [Accepted: 04/29/2024] [Indexed: 10/08/2024] Open
Abstract
Introduction Earthen sites are essential cultural relic resources, and site museums are a fundamental component of China's cultural heritage protection. The mausoleum of the Qin Shi Huang Emperor is one of the largest, most peculiar, and richest imperial tombs in the world. The exhibition hall of the burial pit No. 1 of the Terra Cotta Warriors is the earliest exhibition hall built and opened to the public. However, after years of excavation and open exhibitions, the earthen site of the Emperor Qinshihuang's Mausoleum Site Museum has deteriorated to varying degrees due to changes in the modern environment. There is an urgent need to control microbial diseases and protect the earthen site. Methods We analyzed the physical and chemical properties and bioindicators of the collected soil samples. We also established a metagenomic library and conducted a correlation analysis between microbial community composition and environmental factors. Cultivable fungi obtained from air and soil samples were identified, and allicin volatile gas fungistasis test was conducted. Result Research has found that four different areas of the exhibition hall have different types of microbial diseases owing to their different environments. The main pathogenic fungi in earthen site may lead to potential microbial diseases that affect important cultural relics such as the Terra Cotta Warriors. Penicillium, Aspergillus and Talaromyces showed relatively specific growth in relation to environmental factors and showed a better raw growth advantage.Allicin gas had a inhibitory effect on 12 types of fungi, therefore allicin gas had a potent inhibitory effect on the growth of the most culturable fungal hyphae. Discussion This study provides basic data for the study of microbial diversity in the exhibition hall of Pit No. 1 at the Terracotta Warriors Museum in Emperor Qinshihuang's Mausoleum Site Museum. It provides a reference for future protection work, which is of great significance.
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Affiliation(s)
- Cen Wang
- Key Laboratory of Archaeomaterials and Conservation, Ministry of Education, Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Lilong Hou
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Nan Jiang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yu Wang
- Key Laboratory of Archaeomaterials and Conservation, Ministry of Education, Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Xiaofen Mao
- Emperor Qinshihuang’s Mausoleum Site Museum, Key Scientific Research Base of Ancient Polychrome Pottery Conservation of State Administration of Culture Heritage, Shaanxi Xi’an, China
| | - Ping Zhou
- Emperor Qinshihuang’s Mausoleum Site Museum, Key Scientific Research Base of Ancient Polychrome Pottery Conservation of State Administration of Culture Heritage, Shaanxi Xi’an, China
| | - Yin Xia
- Emperor Qinshihuang’s Mausoleum Site Museum, Key Scientific Research Base of Ancient Polychrome Pottery Conservation of State Administration of Culture Heritage, Shaanxi Xi’an, China
| | - Yuanyuan Wang
- Key Laboratory of Archaeomaterials and Conservation, Ministry of Education, Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Chuyue Chen
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinyu Yang
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Luo
- Emperor Qinshihuang’s Mausoleum Site Museum, Key Scientific Research Base of Ancient Polychrome Pottery Conservation of State Administration of Culture Heritage, Shaanxi Xi’an, China
| | - Jiao Pan
- Key Laboratory of Archaeomaterials and Conservation, Ministry of Education, Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
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Anthony WE, Allison SD, Broderick CM, Chavez Rodriguez L, Clum A, Cross H, Eloe-Fadrosh E, Evans S, Fairbanks D, Gallery R, Gontijo JB, Jones J, McDermott J, Pett-Ridge J, Record S, Rodrigues JLM, Rodriguez-Reillo W, Shek KL, Takacs-Vesbach T, Blanchard JL. From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. ENVIRONMENTAL MICROBIOME 2024; 19:56. [PMID: 39095861 PMCID: PMC11295382 DOI: 10.1186/s40793-024-00599-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
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Affiliation(s)
| | - Steven D Allison
- University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Caitlin M Broderick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | | | - Alicia Clum
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hugh Cross
- National Ecological Observatory Network - Battelle, Boulder, CO, USA
| | | | - Sarah Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Dawson Fairbanks
- University of California Riverside, Riverside, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | | | | | - Jennifer Jones
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Jason McDermott
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA
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Preston LJ, Jungblut AD, Montgomery W, Ballard CJ, Wilbraham J. The Preservation and Spectral Detection of Historic Museum Specimen Microbial Mat Biosignatures Within Martian Dust: Lessons Learned for Mars Exploration and Sample Return. ASTROBIOLOGY 2024; 24:684-697. [PMID: 38979614 DOI: 10.1089/ast.2023.0118] [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: 07/10/2024]
Abstract
The key building blocks for life on Mars could be preserved within potentially habitable paleo-depositional settings with their detection possible by utilizing mid-infrared spectroscopy; however, a definite identification and confirmation of organic or even biological origin will require the samples to be returned to Earth. In the present study, Fourier-transform infrared (FTIR) spectroscopic techniques were used to characterize both mineralogical and organic materials within Mars dust simulant JSC Mars-1 and ancient Antarctic cyanobacterial microbial mats from 1901 to 1904 Discovery Expedition. When FTIR spectroscopy is applied to cyanobacterial microbial mat communities, the resulting spectra will reflect the average biochemical composition of the mats rather than taxa-specific spectral patterns of the individual organisms and can thus be considered as a total chemical analysis of the mat colony. This study also highlights the potential difficulties in the detection of these communities on Mars and which spectral biosignatures will be most detectable within geological substrates. Through the creation and analysis of a suite of dried microbial mat material and Martian dust simulant mixtures, the spectral signatures and wavenumber positions of CHx aliphatic hydrocarbons and the C-O and O-H bands of polysaccharides remained detectable and may be detectable within sample mixtures obtained through Mars Sample Return activities.
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Affiliation(s)
- Louisa J Preston
- Department of Space & Climate Physics, Mullard Space Science Laboratory, University College London, Dorking, United Kingdom
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Wren Montgomery
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Connor J Ballard
- Department of Space & Climate Physics, Mullard Space Science Laboratory, University College London, Dorking, United Kingdom
| | - Jo Wilbraham
- Life Sciences Department, Natural History Museum, London, United Kingdom
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4
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Maza-Márquez P, Lee MD, Bebout BM. Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat. Sci Rep 2024; 14:2561. [PMID: 38297006 PMCID: PMC10831059 DOI: 10.1038/s41598-024-52626-y] [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: 11/12/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.
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Affiliation(s)
- P Maza-Márquez
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA.
- University of Granada, Granada, Spain.
| | - M D Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - B M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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5
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Oliveira LD, Grazziotin FG, Sánchez-Martínez PM, Sasa M, Flores-Villela O, Prudente ALDC, Zaher H. Phylogenetic and morphological evidence reveals the association between diet and the evolution of the venom delivery system in Neotropical goo-eating snakes. SYST BIODIVERS 2023. [DOI: 10.1080/14772000.2022.2153944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Leonardo De Oliveira
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré, São Paulo, 04263-000, Brazil
- Laboratório de Toxinologia Aplicada, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
| | - Felipe Gobbi Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
| | | | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigaciones en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, San José, Costa Rica
| | - Oscar Flores-Villela
- Museo de Zoologia ‘Alfonso L. Herrera’, Faculdad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | | | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré, São Paulo, 04263-000, Brazil
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Rosenzweig AF, Burian J, Brady SF. Present and future outlooks on environmental DNA-based methods for antibiotic discovery. Curr Opin Microbiol 2023; 75:102335. [PMID: 37327680 PMCID: PMC11076179 DOI: 10.1016/j.mib.2023.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Novel antibiotics are in constant demand to combat a global increase in antibiotic-resistant infections. Bacterial natural products have been a long-standing source of antibiotic compounds, and metagenomic mining of environmental DNA (eDNA) has increasingly provided new antibiotic leads. The metagenomic small-molecule discovery pipeline can be divided into three main steps: surveying eDNA, retrieving a sequence of interest, and accessing the encoded natural product. Improvements in sequencing technology, bioinformatic algorithms, and methods for converting biosynthetic gene clusters into small molecules are steadily increasing our ability to discover metagenomically encoded antibiotics. We predict that, over the next decade, ongoing technological improvements will dramatically increase the rate at which antibiotics are discovered from metagenomes.
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Affiliation(s)
- Adam F Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Pessi IS, Popin RV, Durieu B, Lara Y, Tytgat B, Savaglia V, Roncero-Ramos B, Hultman J, Verleyen E, Vyverman W, Wilmotte A. Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genom 2023; 9:mgen001056. [PMID: 37417735 PMCID: PMC10438808 DOI: 10.1099/mgen.0.001056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Rafael V. Popin
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Benoit Durieu
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- Early Life Traces & Evolution-Astrobiology, UR-Astrobiology, University of Liège, Liège, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Valentina Savaglia
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Beatriz Roncero-Ramos
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
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Santos A, Gómez-Espinoza O, Núñez-Montero K, Zárate A, Andreote FD, Pylro VS, Bravo L, Barrientos L. Measuring the effect of climate change in Antarctic microbial communities: toward novel experimental approaches. Curr Opin Biotechnol 2023; 81:102918. [PMID: 36972633 DOI: 10.1016/j.copbio.2023.102918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 03/29/2023]
Abstract
The Antarctic continent is undergoing a rapid warming, affecting microbial communities throughout its ecosystems. This continent is a natural laboratory for studying the effect of climate change, however, assessing the microbial communities' responses to environmental changes is challenging from a methodological point of view. We suggest novel experimental designs, including multivariable assessments that apply multiomics methods in combination with continuous environmental data recording and new warming simulation systems. Moreover, we propose that climate change studies in Antarctica should consider three main objectives, including descriptive studies, short-term temporary adaptation studies, and long-term adaptive evolution studies. This will help us to understand and manage the effects of climate change on the Earth.
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Affiliation(s)
- Andrés Santos
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Olman Gómez-Espinoza
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Kattia Núñez-Montero
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Ana Zárate
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - León Bravo
- Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco 4811230, Chile.
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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Schultz J, Argentino ICV, Kallies R, Nunes da Rocha U, Rosado AS. Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano. Front Microbiol 2022; 13:885557. [PMID: 35602031 PMCID: PMC9114708 DOI: 10.3389/fmicb.2022.885557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 01/19/2023] Open
Abstract
Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.
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Affiliation(s)
- Júnia Schultz
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Alexandre Soares Rosado
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Lezcano MÁ, Sánchez-García L, Quesada A, Carrizo D, Fernández-Martínez MÁ, Cavalcante-Silva E, Parro V. Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses. Front Microbiol 2022; 13:799360. [PMID: 35928160 PMCID: PMC9345047 DOI: 10.3389/fmicb.2022.799360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.
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Affiliation(s)
- María Ángeles Lezcano
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- *Correspondence: María Ángeles Lezcano,
| | | | - Antonio Quesada
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
| | | | | | - Víctor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
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Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review. Int J Mol Sci 2022; 23:ijms23073737. [PMID: 35409097 PMCID: PMC8998989 DOI: 10.3390/ijms23073737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/19/2022] [Accepted: 03/26/2022] [Indexed: 01/19/2023] Open
Abstract
While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.
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Theoret J, Cavedon M, Hegel T, Hervieux D, Schwantje H, Steenweg R, Watters M, Musiani M. Seasonal movements in caribou ecotypes of Western Canada. MOVEMENT ECOLOGY 2022; 10:12. [PMID: 35272704 PMCID: PMC8908644 DOI: 10.1186/s40462-022-00312-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/27/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Several migratory ungulates, including caribou, are dramatically declining. Caribou of the Barren-ground ecotype, which forms its own subspecies, are known to be mainly migratory. By contrast, within the Woodland subspecies, animals of the Boreal ecotype are known to be mainly sedentary, while those within the Northern and Central Mountain ecotypes to be partially migratory, with only some individuals migrating. Promotion of conservation actions (e.g., habitat protection) that are specific to both residents and migrants, as well as to the areas they frequent seasonally (which may be separate for migrants), requires distinguishing migration from other movement behaviours, which might be a challenge. METHODS We aimed at assessing seasonal movement behaviours, including migratory, resident, dispersing, and nomadic, for caribou belonging to the Barren-ground and Woodland subspecies and ecotypes. We examined seasonal displacement, both planar and altitudinal, and seasonal ranges overlap for 366 individuals that were GPS-collared in Northern and Western Canada. Lastly, we assessed the ability of caribou individuals to switch between migratory and non-migratory movement behaviours between years. RESULTS We detected migratory behaviour within each of the studied subspecies and ecotypes. However, seasonal ranges overlap (an index of sedentary behaviour) varied, with proportions of clear migrants (0 overlap) of 40.94% for Barren-ground caribou and 23.34% for Woodland caribou, and of 32.95%, 54.87%, and 8.86% for its Northern Mountain, Central Mountain, and Boreal ecotype, respectively. Plastic switches of individuals were also detected between migratory, resident, dispersing, and nomadic seasonal movements performed across years. CONCLUSIONS Our unexpected findings of marked seasonal movement plasticity in caribou indicate that this phenomenon should be better studied to understand the resilience of this endangered species to habitat and climatic changes. Our results that a substantial proportion of individuals engaged in seasonal migration in all studied ecotypes indicate that caribou conservation plans should account for critical habitat in both summer and winter ranges. Accordingly, conservation strategies are being devised for the Woodland subspecies and its ecotypes, which were found to be at least partially migratory in this study. Our findings that migration is detectable with both planar and altitudinal analyses of seasonal displacement provide a tool to better define seasonal ranges, also in mountainous and hilly environments, and protect habitat there.
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Affiliation(s)
- Jessica Theoret
- Faculty of Environmental Design, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, YT, Y1A 2C6, Canada
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, 4999 98 Ave., Edmonton, AB, T6B 2X3, Canada
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, AB, T8V 6J4, Canada
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC, V9T 6J9, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - Megan Watters
- Land and Resource Specialist, 300 - 10003 110th Avenue, Fort St. John, BC, V1J 6M7, Canada
| | - Marco Musiani
- Department of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, AB, T2N 1N4, Canada.
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Ishara J, Ayagirwe R, Karume K, Mushagalusa GN, Bugeme D, Niassy S, Udomkun P, Kinyuru J. Inventory reveals wide biodiversity of edible insects in the Eastern Democratic Republic of Congo. Sci Rep 2022; 12:1576. [PMID: 35091646 PMCID: PMC8799670 DOI: 10.1038/s41598-022-05607-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/13/2022] [Indexed: 11/09/2022] Open
Abstract
In response to growing food demand, edible insects are perceived as an opportunity to alleviate food insecurity. With its wide edible insects' biodiversity, the Democratic Republic of Congo is one of Africa's most critical entomophagous. This study aimed at giving a first insight on inventory showing diversity, perception, consumption, availability, host plants, harvesting techniques and processing techniques of edible insects in South-Kivu, DRC. It recorded twenty-three edible insects belonging to nine families and five orders, some of which are consumed in the larval, adult, egg and pupa stages. Rhyncophorus phoenicis, Alphitobius diaperinus, Macrotermes subhyalinus and Acheta domesticus were the most preferred edible insects in Fizi Territory, Ruspolia differens and Apis mellifera larvae in Kabare Territory, Imbrasia oyemensis, Imbrasia epimethea, Rhynchophorus ferrugineus and Rhyncophorus phoenicis in Mwenga Territory, Ruspolia differens, Macrotermes subhyalinus, Gryllotalpa africana, Nsike, Nomadacris septemfasciata and A. mellifera larvae in Walungu Territory. Ruspolia differens, I. oyemensis, A. mellifera larvae, G. africana and Nsike, were preferred for their taste. Acheta domesticus, A. diaperinus and A. mellifera larvae were abundant throughout the year, while others were only available for 9 months or less per year. Numerous plants have been recorded as their hosts, including plants used for food and income. Harvesting strategies and period, processing methods and preservation techniques depend on insect species, local knowledge and practices. These findings suggest similar and thorough studies on entomophagy across the country while encouraging the rearing of edible insects to address their existing high demand and environmental concerns.
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Affiliation(s)
- Jackson Ishara
- Department of Food Science and Technology, Université Evangélique en Afrique, P.O. Box 3323, Bukavu, Democratic Republic of Congo.
- Department of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Rodrigue Ayagirwe
- Department of Animal Sciences, Université Evangélique en Afrique, P.O. Box: 3323, Bukavu, Democratic Republic of Congo
| | - Katcho Karume
- Department of Crop Sciences, Université Evangélique en Afrique, P.O. Box: 3323, Bukavu, Democratic Republic of Congo
| | - Gustave N Mushagalusa
- Department of Crop Sciences, Université Evangélique en Afrique, P.O. Box: 3323, Bukavu, Democratic Republic of Congo
| | - David Bugeme
- Crop Production and Protection Unit, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Saliou Niassy
- International Centre of Insect Physiology and Ecology (Icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | | | - John Kinyuru
- Department of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
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KINASZ CAMILAT, KREUSCH MARIANNEG, BENDIA AMANDAG, PELLIZARI VIVIANH, DUARTE RUBENST. Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection. AN ACAD BRAS CIENC 2022; 94:e20210621. [DOI: 10.1590/0001-3765202220210621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
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Griffioen M, Iserbyt A, Müller W. Turn taking is not restricted by task specialisation but does not facilitate equality in offspring provisioning. Sci Rep 2021; 11:21884. [PMID: 34750443 PMCID: PMC8575876 DOI: 10.1038/s41598-021-01298-z] [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: 04/07/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
Sexual conflict arises when two individuals invest in their common offspring because both individuals benefit when their partner invests more. Conditional cooperation is a theoretical concept that could resolve this conflict. Here, parents are thought to motivate each other to contribute to provisioning visits by following the rules of turn taking, which results in equal and efficient investment. However, parents have other tasks besides provisioning, which might hinder taking turns. To investigate restrictions by other care tasks and whether turn taking can be used to match investment, we manipulated brooding duration in female blue tits (Cyanistes caeruleus) during the early nestling phase by changing nest box temperature. As expected, females subjected to cold conditions brooded longer than females under warm conditions. Yet, contrary to our prediction, females had similar visit rates in both treatments, which suggests that females in the cold treatment invested more overall. In addition, the females' turn taking level was higher in the more demanding cold condition (and the calculated randomised turn taking levels of females did not differ), hence females don't seem to be restricted in their turn taking strategy by other care tasks. However, males did not seem to match the females' turn taking levels because they did not adjust their visit rates. Thus, level of turn taking was not restricted by an other sex-specific task in females and did not facilitate a greater investment by their male partners.
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Affiliation(s)
- Maaike Griffioen
- Department of Biology, Behavioural Ecology and Ecophysiology Research Group, University of Antwerp, Wilrijk, Belgium.
| | - Arne Iserbyt
- grid.5284.b0000 0001 0790 3681Department of Biology, Behavioural Ecology and Ecophysiology Research Group, University of Antwerp, Wilrijk, Belgium
| | - Wendt Müller
- grid.5284.b0000 0001 0790 3681Department of Biology, Behavioural Ecology and Ecophysiology Research Group, University of Antwerp, Wilrijk, Belgium
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17
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Zeppelini CG, Carvalho-Pereira T, Alves RS, Santiago DCC, Santo VFE, Begon M, Costa F, Khalil H. Demographic drivers of Norway rat populations from urban slums in Brazil. Urban Ecosyst 2021; 24:801-809. [PMID: 34720572 PMCID: PMC8550123 DOI: 10.1007/s11252-020-01075-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 11/27/2022]
Abstract
The Norway rat is a globally distributed pest, known for its resilience to eradication and control programs. Efficient population control, especially in urban settings, is dependent on knowledge of rat demography and population ecology. We analyzed the relationship between four demographic outcomes, estimated by live-trapping data, and fine-scale environmental features measured at the capture site. Wounds, a proxy for agonistic interactions, were associated with mature individuals. Areas with environmental features favorable to rats, such as open sewers and unpaved earth, were associated with more mature individuals with a better body condition index. The control measures (environmental stressors) are likely to be disrupting the social structure of rat colonies, increasing the frequency and distribution of agonistic interactions, which were common in both sexes and maturity states. The relationship between the favorable environmental conditions and the demographic markers analyzed indicate possible targets for infestation control through environmental manipulation, and could be incorporated into current pest management programs to achieve long-term success. Our study indicate that urban interventions focused on removal of potential resources for rats could be potential long-term solutions by reducing the carrying capacity of the environment. Supplementary Information The online version contains supplementary material available at 10.1007/s11252-020-01075-2.
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Affiliation(s)
- C G Zeppelini
- Laboratório de Mamíferos, Universidade Federal da Paraíba, Cidade Universitária, João Pessoa, Brazil.,Programa de Pós-Graduação em Ecologia: Teoria, Aplicações e Valores, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - T Carvalho-Pereira
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, R. Basílio da Gama, S/N, Salvador, Brazil
| | - R Sady Alves
- Programa de Pós-Graduação em Ciência Animal nos Trópicos, Universidade federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - D C C Santiago
- Instituto de Biologia, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - V F Espirito Santo
- Faculdade de Farmácia, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - M Begon
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB UK
| | - F Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, R. Basílio da Gama, S/N, Salvador, Brazil
| | - Hussein Khalil
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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18
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Antelo V, Giménez M, Azziz G, Valdespino‐Castillo P, Falcón LI, Ruberto LAM, Mac Cormack WP, Mazel D, Batista S. Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment. Microbiologyopen 2021; 10:e1219. [PMID: 34713606 PMCID: PMC8435808 DOI: 10.1002/mbo3.1219] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/24/2021] [Indexed: 11/08/2022] Open
Abstract
The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.
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Affiliation(s)
- Verónica Antelo
- Laboratorio de Microbiología MolecularInstituto de Investigaciones Biológicas Clemente Estable (MECAv. Italia 3318MontevideoCP 11600Uruguay
| | - Matías Giménez
- Laboratorio de Microbiología MolecularInstituto de Investigaciones Biológicas Clemente Estable (MECAv. Italia 3318MontevideoCP 11600Uruguay
- Laboratorio de Genómica MicrobianaInstitut Pasteur Montevideo. Mataojo 2020MontevideoUruguay
| | - Gastón Azziz
- Laboratorio de MicrobiologíaFacultad de AgronomíaUdelaR. Av. Garzón 780. CP 12900MontevideoUruguay
| | - Patricia Valdespino‐Castillo
- Molecular Biophysics and Integrated Bioimaging DivisionBSISB ProgramLawrence Berkeley National LaboratoryOne Cyclotron RdBerkeleyCA94720USA
| | - Luisa I. Falcón
- Laboratorio de Ecología BacterianaInstituto de EcologíaUniversidad Nacional Autónoma de MéxicoCDMX04510Mexico
- UNAMParque Científico y Tecnológico de Yucatán97302Mexico
| | - Lucas A. M. Ruberto
- Instituto Antártico Argentino. Av25 de Mayo 1143San Martín, Buenos Aires1650Argentina
- Cátedra de BiotecnologíaFacultad de Farmacia y Bioquímica e Instituto Nanobiotec UBA‐CONICET. Ave. Junín 956Buenos Aires1113Argentina
| | - Walter P. Mac Cormack
- Instituto Antártico Argentino. Av25 de Mayo 1143San Martín, Buenos Aires1650Argentina
- Cátedra de BiotecnologíaFacultad de Farmacia y Bioquímica e Instituto Nanobiotec UBA‐CONICET. Ave. Junín 956Buenos Aires1113Argentina
| | - Didier Mazel
- Département Génomes et GénétiqueInstitut PasteurUnité Plasticité du Génome BactérienParisFrance
- CNRSUMR3525ParisFrance
| | - Silvia Batista
- Laboratorio de Microbiología MolecularInstituto de Investigaciones Biológicas Clemente Estable (MECAv. Italia 3318MontevideoCP 11600Uruguay
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Kavelaars MM, Baert JM, Van Malderen J, Stienen EWM, Shamoun-Baranes J, Lens L, Müller W. Simultaneous GPS-tracking of parents reveals a similar parental investment within pairs, but no immediate co-adjustment on a trip-to-trip basis. MOVEMENT ECOLOGY 2021; 9:42. [PMID: 34419142 PMCID: PMC8379723 DOI: 10.1186/s40462-021-00279-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Parental care benefits the offspring, but comes at a cost for each parent, which in biparental species gives rise to a conflict between partners regarding the within-pair distribution of care. Pair members could avoid exploitation by efficiently keeping track of each other's efforts and coordinating their efforts. Parents may, therefore, space their presence at the nest, which could also allow for permanent protection of the offspring. Additionally, they may respond to their partner's previous investment by co-adjusting their efforts on a trip-to-trip basis, resulting in overall similar parental activities within pairs. METHODS We investigated the coordination of parental care measured as nest attendance and foraging effort in the Lesser black-backed gull (Larus fuscus), a species with long nest bouts that performs extended foraging trips out of sight of their partner. This was achieved by GPS-tracking both pair members simultaneously during the entire chick rearing period. RESULTS We found that the timing of foraging trips (and hence nest attendance) was coordinated within gull pairs, as individuals left the colony only after their partner had returned. Parents did not match their partner's investment by actively co-adjusting their foraging efforts on a trip-by-trip basis. Yet, pair members were similar in their temporal and energetic investments during chick rearing. CONCLUSION Balanced investment levels over a longer time frame suggest that a coordination of effort may not require permanent co-adjustment of the levels of care on a trip-to-trip basis, but may instead rather take place at an earlier stage in the reproductive attempt, or over integrated longer time intervals. Identifying the drivers and underlying processes of coordination will be one of the next necessary steps to fully understand parental cooperation in long-lived species.
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Affiliation(s)
- Marwa M Kavelaars
- Behavioural Ecology and Ecophysiology Group (BECO), University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Terrestrial Ecology Unit (TEREC), Ghent University, K.L, Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Jan M Baert
- Behavioural Ecology and Ecophysiology Group (BECO), University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
- Terrestrial Ecology Unit (TEREC), Ghent University, K.L, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Jolien Van Malderen
- Terrestrial Ecology Unit (TEREC), Ghent University, K.L, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Eric W M Stienen
- Research Institute for Nature and Forest (INBO), Havenlaan 88, 1000, Brussels, Belgium
| | - Judy Shamoun-Baranes
- Theoretical and Computational Ecology, IBED, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Luc Lens
- Terrestrial Ecology Unit (TEREC), Ghent University, K.L, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Wendt Müller
- Behavioural Ecology and Ecophysiology Group (BECO), University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
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Murray MH, Byers KA, Buckley J, Magle SB, Maffei D, Waite P, German D. "I don't feel safe sitting in my own yard": Chicago resident experiences with urban rats during a COVID-19 stay-at-home order. BMC Public Health 2021; 21:1008. [PMID: 34049525 PMCID: PMC8163585 DOI: 10.1186/s12889-021-11095-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Encounters with rats in urban areas increase risk of human exposure to rat-associated zoonotic pathogens and act as a stressor associated with psychological distress. The frequency and nature of human-rat encounters may be altered by social distancing policies to mitigate the COVID-19 pandemic. For example, restaurant closures may reduce food availability for rats and promote rat activity in nearby residential areas, thus increasing public health risks during a period of public health crisis. In this study, we aimed to identify factors associated with increased perceived exposure to rats during a stay-at-home order, describe residents' encounters with rats relevant to their health and well-being, and identify factors associated with increased use of rodent control. METHODS Urban residents in Chicago, a large city with growing concerns about rats and health disparities, completed an online questionnaire including fixed response and open-ended questions during the spring 2020 stay-at-home order. Analyses included ordinal multivariate regression, spatial analysis, and thematic analysis for open-ended responses. RESULTS Overall, 21% of respondents (n = 835) reported an increase in rat sightings around their homes during the stay-at-home order and increased rat sightings was positively associated with proximity to restaurants, low-rise apartment buildings, and rat feces in the home (p ≤ 0.01). Many respondents described feeling unsafe using their patio or yard, and afraid of rats entering their home or spreading disease. Greater engagement with rodent control was associated with property ownership, information about rat control, and areas with lower incomes (p ≤ 0.01). CONCLUSIONS More frequent rat encounters may be an unanticipated public health concern during periods of social distancing, especially in restaurant-dense areas or in low-rise apartment buildings. Rat presence may also limit residents' ability to enjoy nearby outdoor spaces, which otherwise might buffer stress experienced during a stay-at-home order. Proactive rat control may be needed to mitigate rat-associated health risks during future stay-at-home orders.
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Affiliation(s)
- Maureen H Murray
- Urban Wildlife Institute, Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA.
| | - Kaylee A Byers
- Department of Interdisciplinary Studies, University of British Columbia, Vancouver, British Columbia, Canada.,Canadian Wildlife Health Cooperative, Animal Health Centre, Abbotsford, BC, Canada
| | - Jacqueline Buckley
- Urban Wildlife Institute, Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Seth B Magle
- Urban Wildlife Institute, Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Dorothy Maffei
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Preeya Waite
- Center for Community Health Equity, DePaul University, Chicago, IL, USA
| | - Danielle German
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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21
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Ramoneda J, Hawes I, Pascual-García A, J Mackey T, Y Sumner D, D Jungblut A. Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system. FEMS Microbiol Ecol 2021; 97:6174672. [PMID: 33729491 DOI: 10.1093/femsec/fiab044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/14/2021] [Indexed: 11/14/2022] Open
Abstract
Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA gene sequencing, we evaluated microbial mat and planktonic communities within a connected freshwater system in the McMurdo Wright Valley, Antarctica, to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined communities from glacial Lake Brownworth, the perennially ice-covered Lake Vanda and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar. Despite the higher physical connectivity and dispersal opportunities between bacterial communities in the shallow parts of the system, environmental abiotic conditions dominated over dispersal in driving community structure. Functional metabolic pathway predictions suggested differences in the functional gene potential between the microbial mat communities located in shallower and deeper water depths. The findings suggest that increasing temperatures and meltwater due to future climate change will affect bacterial diversity and functioning in Antarctic freshwater ecosystems.
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Affiliation(s)
- Josep Ramoneda
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Tauranga 3110, New Zealand
| | - Alberto Pascual-García
- Theoretical Biology, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich 8006, Switzerland
| | - Tyler J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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22
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Perez-Mon C, Qi W, Vikram S, Frossard A, Makhalanyane T, Cowan D, Frey B. Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). Microb Genom 2021; 7:000558. [PMID: 33848236 PMCID: PMC8208683 DOI: 10.1099/mgen.0.000558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Carla Perez-Mon,
| | - Weihong Qi
- Functional Genomics Center of the University of Zurich and the ETH Zurich, Zurich, Switzerland
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Thulani Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
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Oyewusi HA, Abdul Wahab R, Edbeib MF, Mohamad MAN, Abdul Hamid AA, Kaya Y, Huyop F. Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1840437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
| | - Mohamed Faraj Edbeib
- Faculty of Medical Technology, Department of Medical Laboratories, Baniwalid University, Baniwalid, Libya
| | - Mohd Azrul Naim Mohamad
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
| | - Yilmaz Kaya
- Agriculture Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Agriculture Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
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Are antimicrobial resistance genes key targets to detect genetically modified microorganisms in fermentation products? Int J Food Microbiol 2020; 331:108749. [PMID: 32622259 DOI: 10.1016/j.ijfoodmicro.2020.108749] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/05/2020] [Accepted: 06/06/2020] [Indexed: 11/21/2022]
Abstract
As genetically modified microorganisms (GMM), commonly used by the food and feed industry to produce additives, enzymes and flavourings, are frequently harbouring antimicrobial resistance (AMR) genes as selection markers, health and environmental concerns were consequently raised. For this reason, the interest of the competent authorities to control such microbial fermentation products has strongly increased, especially since several recent accidental contaminations of unauthorized GMM, or associated recombinant DNA, in bacterial fermentation products intended for the European food and feed chain. However, no global screening strategy is currently available in enforcement laboratories to assess the presence of GMM harbouring AMR genes and/or the presence of full-length AMR genes. Moreover, the confidentiality of the related GMM dossiers strongly hampers the development of methods to perform such control. To overcome this issue, an analysis of related publicly available patents was performed in this study to identify all reported AMR genes. On this basis, the aminoglycoside adenyltransferase (aadD) gene, conferring a resistance to both kanamycin and neomycin, was identified as a key target to cover a large spectrum of GM bacteria. A real-time PCR method to screen for its potential presence as well as a nested-PCR method associated with a sequencing analysis to assess its full-length were developed to target this aadD gene. The performance of these new methods were successfully evaluated in terms of specificity, sensitivity and applicability, allowing their easy implementation in enforcement laboratories. Moreover, the integration of these newly developed methods to our very recently proposed strategy, initially targeting GMM carrying a chloramphenicol resistance gene, allows to drastically increase the detection spectrum of GM bacteria producing fermentation food and feed products. The data generated by the proposed strategy represents therefore a crucial support for the competent authorities, especially to evaluate potential risks for the food and feed safety.
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Anderson CM, Gilchrist HG, Ronconi RA, Shlepr KR, Clark DE, Fifield DA, Robertson GJ, Mallory ML. Both short and long distance migrants use energy-minimizing migration strategies in North American herring gulls. MOVEMENT ECOLOGY 2020; 8:26. [PMID: 32549986 PMCID: PMC7294659 DOI: 10.1186/s40462-020-00207-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/27/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Recent studies have proposed that birds migrating short distances migrate at an overall slower pace, minimizing energy expenditure, while birds migrating long distances minimize time spent on migration to cope with seasonal changes in environmental conditions. METHODS We evaluated variability in the migration strategies of Herring Gulls (Larus argentatus), a generalist species with flexible foraging and flight behaviour. We tracked one population of long distance migrants and three populations of short distance migrants, and compared the directness of their migration routes, their overall migration speed, their travel speed, and their use of stopovers. RESULTS Our research revealed that Herring Gulls breeding in the eastern Arctic migrate long distances to spend the winter in the Gulf of Mexico, traveling more than four times farther than gulls from Atlantic Canada during autumn migration. While all populations used indirect routes, the long distance migrants were the least direct. We found that regardless of the distance the population traveled, Herring Gulls migrated at a slower overall migration speed than predicted by Optimal Migration Theory, but the long distance migrants had higher speeds on travel days. While long distance migrants used more stopover days overall, relative to the distance travelled all four populations used a similar number of stopover days. CONCLUSIONS When taken in context with other studies, we expect that the migration strategies of flexible generalist species like Herring Gulls may be more influenced by habitat and food resources than migration distance.
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Affiliation(s)
- Christine M. Anderson
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS B4P 2R6 Canada
| | - H. Grant Gilchrist
- Wildlife Research Division, Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON K1S 5B6 Canada
| | - Robert A. Ronconi
- Canadian Wildlife Service, Environment and Climate Change Canada, 45 Alderney Dr, Dartmouth, NS B2Y 2N6 Canada
| | - Katherine R. Shlepr
- Atlantic Lab for Avian Research, Department of Biology, University of New Brunswick, P.O. Box 4400, 10 Bailey Drive, Fredericton, NB E3B 5A3 Canada
| | - Daniel E. Clark
- Massachusetts Department of Conservation and Recreation, Division of Water Supply Protection, 485 Ware Road, Belchertown, MA 01007 USA
| | - David A. Fifield
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3 Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3 Canada
| | - Mark L. Mallory
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS B4P 2R6 Canada
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Bøifot KO, Gohli J, Moen LV, Dybwad M. Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research. ENVIRONMENTAL MICROBIOME 2020; 15:1. [PMID: 33902731 PMCID: PMC8067373 DOI: 10.1186/s40793-019-0349-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 12/03/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Aerosol microbiome research advances our understanding of bioaerosols, including how airborne microorganisms affect our health and surrounding environment. Traditional microbiological/molecular methods are commonly used to study bioaerosols, but do not allow for generic, unbiased microbiome profiling. Recent studies have adopted shotgun metagenomic sequencing (SMS) to address this issue. However, SMS requires relatively large DNA inputs, which are challenging when studying low biomass air environments, and puts high requirements on air sampling, sample processing and DNA isolation protocols. Previous SMS studies have consequently adopted various mitigation strategies, including long-duration sampling, sample pooling, and whole genome amplification, each associated with some inherent drawbacks/limitations. RESULTS Here, we demonstrate a new custom, multi-component DNA isolation method optimized for SMS-based aerosol microbiome research. The method achieves improved DNA yields from filter-collected air samples by isolating DNA from the entire filter extract, and ensures a more comprehensive microbiome representation by combining chemical, enzymatic and mechanical lysis. Benchmarking against two state-of-the-art DNA isolation methods was performed with a mock microbial community and real-world air samples. All methods demonstrated similar performance regarding DNA yield and community representation with the mock community. However, with subway samples, the new method obtained drastically improved DNA yields, while SMS revealed that the new method reported higher diversity. The new method involves intermediate filter extract separation into a pellet and supernatant fraction. Using subway samples, we demonstrate that supernatant inclusion results in improved DNA yields. Furthermore, SMS of pellet and supernatant fractions revealed overall similar taxonomic composition but also identified differences that could bias the microbiome profile, emphasizing the importance of processing the entire filter extract. CONCLUSIONS By demonstrating and benchmarking a new DNA isolation method optimized for SMS-based aerosol microbiome research with both a mock microbial community and real-world air samples, this study contributes to improved selection, harmonization, and standardization of DNA isolation methods. Our findings highlight the importance of ensuring end-to-end sample integrity and using methods with well-defined performance characteristics. Taken together, the demonstrated performance characteristics suggest the new method could be used to improve the quality of SMS-based aerosol microbiome research in low biomass air environments.
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Affiliation(s)
- Kari Oline Bøifot
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK
| | - Jostein Gohli
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Line Victoria Moen
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Marius Dybwad
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway.
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK.
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Greenfield SR, Tighe SW, Bai Y, Goerlitz DS, Von Turkovich M, Taatjes DJ, Dragon JA, Johnson SS. Life and its traces in Antarctica's McMurdo Dry Valley paleolakes: a survey of preservation. Micron 2019; 131:102818. [PMID: 31968300 DOI: 10.1016/j.micron.2019.102818] [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: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 01/21/2023]
Abstract
The extremely cold and arid conditions of Antarctica make it uniquely positioned to investigate fundamental questions regarding the persistence of life in extreme environments. Within the McMurdo Dry Valleys and surrounding mountain ranges are multiple ancient relict lakes, paleolakes, with lacustrine deposits spanning from thousands to millions of years in age. Here we present data from light microscopy, scanning electron microscopy, electron dispersive x-ray spectroscopy, and radiocarbon dating to catalog the remarkable range of life preserved within these deposits. This includes intact microbes and nanobacteria-sized cocci, CaCO3 precipitations consistent with biogenic calcium, previously undescribed net-like structures, possible dormant spores, and long-extinct yet exquisitely preserved non-vascular plants. These images provide an important reference for further microbiome investigations of Antarctic paleolake samples. In addition, these findings may provide a visual reference for the use of subsurface groundwater microbial communities as an analog for paleolake subsurface water on planets such as Mars.
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Affiliation(s)
| | - Scott W Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, VT, 05405 USA
| | - Yu Bai
- Department of Biology, Georgetown University, Washington DC 20057 USA
| | - David S Goerlitz
- Georgetown University Medical Center, Georgetown University, Washington DC, 20057 USA
| | - Michele Von Turkovich
- Department of Pathology and Laboratory Medicine, USA; Microscopy Imaging Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405 USA
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, USA; Microscopy Imaging Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405 USA
| | - Julie A Dragon
- Vermont Integrative Genomics, University of Vermont, Burlington, VT, 05405 USA; Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, 05405 USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington DC 20057 USA; Science, Technology, and International Affairs Program, Georgetown University, Washington DC, 20057 USA
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Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
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Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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