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Sierra MA, Ryon KA, Tierney BT, Foox J, Bhattacharya C, Afshin E, Butler D, Green SJ, Thomas WK, Ramsdell J, Bivens NJ, McGrath K, Mason CE, Tighe SW. Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations. Environ Microbiome 2022; 17:60. [PMID: 36544228 PMCID: PMC9768965 DOI: 10.1186/s40793-022-00455-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.
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Affiliation(s)
- Maria A Sierra
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Krista A Ryon
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Braden T Tierney
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jonathan Foox
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Evan Afshin
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, New York, IL, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | | | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, USA
| | | | - Christopher E Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Scott W Tighe
- Advanced Genomics Laboratory, University of Vermont Cancer Center, University of Vermont, Burlington, VT, USA.
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Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, Gibas C, Bezdan D, Deng Y, He D, Dias-Neto E, Elhaik E, Afshin E, Grills G, Iraola G, Suzuki H, Werner J, Udekwu K, Schriml L, Bhattacharyya M, Oliveira M, Zambrano MM, Hazrin-Chong NH, Osuolale O, Łabaj PP, Tiasse P, Rapuri S, Borras S, Pozdniakova S, Shi T, Sezerman U, Rodo X, Sezer ZH, Mason CE. A history of the MetaSUB consortium: Tracking urban microbes around the globe. iScience 2022; 25:104993. [PMID: 36299999 PMCID: PMC9589169 DOI: 10.1016/j.isci.2022.104993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
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Affiliation(s)
- Krista A. Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
- Kyiv Academic University, Kyiv, Ukraine
| | - Andre Kahles
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christelle Desnues
- Mediterranean Institute of Oceanography, 163 Avenue de Luminy Bâtiment Méditerranée, 13288, Marseille Cedex 9, France
| | | | | | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- GermanyNGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- yuri GmbH, Meckenbeuren, Germany
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ding He
- University of Copenhagen, Copenhagen, Denmark
| | | | | | - Evan Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Gregorio Iraola
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | | | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Klas Udekwu
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lynn Schriml
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | | | | | | | | | | | | | | | - Sampath Rapuri
- The Community Lab; Los Alamos Makers, Los Alamos, NM 87544, USA
| | - Silvia Borras
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Sofya Pozdniakova
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Tieliu Shi
- East China Normal University, Zhongshan Rd (N), 3663, 200050 Shanghai, Putuo, China
| | - Ugur Sezerman
- Department of Biostatistics, Acibadem University, Istanbul, Turkey
| | - Xavier Rodo
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
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