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Cecchetto M, Di Cesare A, Eckert E, Fassio G, Fontaneto D, Moro I, Oliverio M, Sciuto K, Tassistro G, Vezzulli L, Schiaparelli S. Antarctic coastal nanoplankton dynamics revealed by metabarcoding of desalination plant filters: Detection of short-term events and implications for routine monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143809. [PMID: 33257075 DOI: 10.1016/j.scitotenv.2020.143809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
One of the main requirements of any sound biological monitoring is the availability of long term and, possibly, temporal data with a high resolution. This is often difficult to be achieved, especially in Antarctica, due to a variety of logistic constraints, which make continuous sampling and monitoring activities generally unfeasible. Here we focus on the 5 μm filters used in the desalination plant of the Italian research base "Mario Zucchelli" in the Terra Nova Bay area (Ross Sea, Antarctica) to evaluate intra-annual coastal nanoplankton dynamics. These filters, together with others of larger mesh sizes, are used to decrease the amount of organisms and debris in the input seawater before the desalination processes take place, hence automatically collect the plankton present in the water column around the desalination system intake. We have used a DNA metabarcoding approach to characterize the communities retained by filters' sets collected in January 2012 and 2013. Intra-annual dynamics were disclosed with an unprecedented detail, that would not have been possible by using standard sampling approaches, and highlighted the importance of extreme, stochastic events such as katabatic wind pulses, which triggered dramatic, short-term shifts in coastal nanoplankton composition. This method, by combining a cost-effective sampling and molecular techniques, may represent a viable solution for long-term monitoring programs focusing on Antarctic coastal communities.
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Affiliation(s)
- Matteo Cecchetto
- Italian National Antarctic Museum (MNA, Section of Genoa), University of Genoa, Genoa, Italy; Department of Earth, Environmental and Life Science (DISTAV), University of Genoa, Genoa, Italy.
| | - Andrea Di Cesare
- National Research Council of Italy, Water Research Institute (CNR-IRSA), Verbania Pallanza, Italy
| | - Ester Eckert
- National Research Council of Italy, Water Research Institute (CNR-IRSA), Verbania Pallanza, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Diego Fontaneto
- National Research Council of Italy, Water Research Institute (CNR-IRSA), Verbania Pallanza, Italy
| | - Isabella Moro
- Department of Biology, University of Padova, Padua, Italy
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Katia Sciuto
- Department of Biology, University of Padova, Padua, Italy
| | - Giovanni Tassistro
- Department of Earth, Environmental and Life Science (DISTAV), University of Genoa, Genoa, Italy
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Science (DISTAV), University of Genoa, Genoa, Italy
| | - Stefano Schiaparelli
- Italian National Antarctic Museum (MNA, Section of Genoa), University of Genoa, Genoa, Italy; Department of Earth, Environmental and Life Science (DISTAV), University of Genoa, Genoa, Italy
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Linard B, Swenson K, Pardi F. Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics 2020; 35:3303-3312. [PMID: 30698645 DOI: 10.1093/bioinformatics/btz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing. RESULTS We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics. AVAILABILITY AND IMPLEMENTATION Program and sources freely available for download at https://github.com/blinard-BIOINFO/RAPPAS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,ISEM, University of Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRA, Montpellier Supagro, Montpellier, France
| | - Krister Swenson
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,Institut de Biologie Computationnelle, Montpellier, France
| | - Fabio Pardi
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,Institut de Biologie Computationnelle, Montpellier, France
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Shamarina D, Stoyantcheva I, Mason CE, Bibby K, Elhaik E. Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research. MICROBIOME 2017; 5:132. [PMID: 28978331 PMCID: PMC5628477 DOI: 10.1186/s40168-017-0349-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/20/2017] [Indexed: 05/07/2023]
Abstract
The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.
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Affiliation(s)
- Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Iana Stoyantcheva
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021 USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Kyle Bibby
- University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dameᅟ, IN 46556 USA
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN UK
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