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Targueta CP, Antunes AM, Machado KB, Fernandes JG, Telles MPDEC, Vieira LCG, Logares R, Nabout JC, Soares TN. Diversity of eukaryotic and prokaryotic microbiota revealed by metabarcoding in Neotropical floodplain lakes. AN ACAD BRAS CIENC 2023; 95:e20201578. [PMID: 37585965 DOI: 10.1590/0001-3765202320201578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 08/18/2023] Open
Abstract
The diversity of eukaryotic and prokaryotic communities has been assessed by morphological and genetic approaches, which are used to characterize the microbiota in different environments. Here, planktonic prokaryotic and eukaryotic communities of the Araguaia River, located in the Central region of Brazil, were analyzed based on metabarcoding analysis of rRNA genes to evaluate the diversity of these groups in tropical floodplain lakes. Also, we tested their spatial concordance throughout the Araguaia river. Water samples were collected from 8 floodplain lakes in Araguaia River. The 16S and 18S rRNA genes were amplified and sequenced using Illumina MiSeq. For eukaryotes, 34,242 merged reads were obtained and 225 distinct OTUs were delineated, of which 106 OTUs were taxonomically classified. For prokaryotes, 26,426 sequences were obtained and 351 OTUs were detected. Of them, 231 were classified in at least one taxonomic category. The most representative eukaryotes belonged to Ciliophora, Chlorophyta and Charophyta. The prokaryotic phylum with the most OTUs classified were Proteobacteria, Actinobacteria and Bacteroidetes. The lakes did not show spatial concordance when comparing the similarity between their microbiota. The knowledge of freshwater biodiversity using DNA sequencing for important rivers, such as Araguaia River, can improve microbiota inventories of tropical biodiversity hotspots.
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Affiliation(s)
- Cíntia P Targueta
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Adriana M Antunes
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Karine B Machado
- Universidade Estadual de Goiás (UEG), Campus Central, BR 153, Fazenda Barreiro do Meio, N° 3105, 75132-903 Anápolis, GO, Brazil
| | - Jordana G Fernandes
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Rua 235, 722, Setor Leste Universitário, 74605-050 Goiânia, GO, Brazil
| | - Mariana P DE C Telles
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Rua 235, 722, Setor Leste Universitário, 74605-050 Goiânia, GO, Brazil
| | - Ludgero C Galli Vieira
- Universidade de Brasília (UnB), Campus Planaltina, Área Universitária 1, Vila Nossa Senhora de Fátima, 73345-010 Planaltina, DF, Brazil
| | - Ramiro Logares
- Instituto de Ciências del Mar, Departamento de Biologia Marinha e Oceanografia CSIC, 08003, Barcelona, Spain
| | - João C Nabout
- Universidade Estadual de Goiás (UEG), Campus Central, BR 153, Fazenda Barreiro do Meio, N° 3105, 75132-903 Anápolis, GO, Brazil
| | - Thannya N Soares
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
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Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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Gionchetta G, Oliva F, Romaní AM, Bañeras L. Hydrological variations shape diversity and functional responses of streambed microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136838. [PMID: 32018979 DOI: 10.1016/j.scitotenv.2020.136838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/08/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.
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Affiliation(s)
- G Gionchetta
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain.
| | - F Oliva
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A M Romaní
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain
| | - L Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain
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Voss C, Fiore-Donno AM, Guerreiro MA, Peršoh D, Bonkowski M. Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage. FEMS Microbiol Ecol 2019; 95:5565044. [DOI: 10.1093/femsec/fiz142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
ABSTRACTForest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.
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Affiliation(s)
- Christian Voss
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Marco Alexandre Guerreiro
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Derek Peršoh
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
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Shackleton M, Rees GN, Watson G, Campbell C, Nielsen D. Environmental DNA reveals landscape mosaic of wetland plant communities. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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8
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Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS Microbiol Rev 2019; 43:415-434. [DOI: 10.1093/femsre/fuz011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
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Affiliation(s)
- Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Marie-Hélène Rodier
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Estelle Cateau
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
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Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L. Towards robust and repeatable sampling methods in eDNA-based studies. Mol Ecol Resour 2018; 18:940-952. [PMID: 29802793 DOI: 10.1111/1755-0998.12907] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/28/2023]
Abstract
DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.
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Affiliation(s)
- Ian A Dickie
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Stephane Boyer
- Institut de Recherche sur la Biologie de l'Insecte - UMR 7261 CNRS, Université de Tours, Tours, France
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, CHARS Campus, Cambridge Bay, NU, Canada
| | | | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Andreas Makiola
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
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Röhl O, Graupner N, Peršoh D, Kemler M, Mittelbach M, Boenigk J, Begerow D. Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities. MICROBIAL ECOLOGY 2018; 75:875-887. [PMID: 29026984 DOI: 10.1007/s00248-017-1085-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 05/22/2023]
Abstract
The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.
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Affiliation(s)
- Oliver Röhl
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Nadine Graupner
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Derek Peršoh
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Martin Kemler
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Moritz Mittelbach
- AG Ökologie der Pflanzen; Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
| | - Jens Boenigk
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Begerow
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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Geisen S. Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists. Environ Microbiol 2018; 18:1669-72. [PMID: 27059550 DOI: 10.1111/1462-2920.13309] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute for Ecology, Wageningen, The Netherlands
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12
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Fiore-Donno AM, Rixen C, Rippin M, Glaser K, Samolov E, Karsten U, Becker B, Bonkowski M. New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol Ecol Resour 2017; 18:229-239. [PMID: 29058814 DOI: 10.1111/1755-0998.12729] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/31/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists, and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hypervariable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (c. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new-generation sequencing primers. In mountain grassland soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 operational taxonomic units (OTUs) at 97% similarity threshold from 26 samples, with c. 50,000 sequences per site, and only 8% of noncercozoan sequences. We could report a further increase in the diversity of Cercozoa, as only 43% of the OTUs were 97%-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
| | - Christian Rixen
- Institute for Snow and Avalanche Research SLF, Davos Dorf, Switzerland
| | - Martin Rippin
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Karin Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Elena Samolov
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Burkhard Becker
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
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13
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Rolls RJ, Heino J, Ryder DS, Chessman BC, Growns IO, Thompson RM, Gido KB. Scaling biodiversity responses to hydrological regimes. Biol Rev Camb Philos Soc 2017; 93:971-995. [DOI: 10.1111/brv.12381] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 09/24/2017] [Accepted: 10/02/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Robert J. Rolls
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
- School of Environmental and Rural Science; University of New England; Armidale New South Wales 2351 Australia
| | - Jani Heino
- Finnish Environment Institute, Natural Environment Centre, Biodiversity; Oulu Finland
| | - Darren S. Ryder
- School of Environmental and Rural Science; University of New England; Armidale New South Wales 2351 Australia
| | | | - Ivor O. Growns
- School of Environmental and Rural Science; University of New England; Armidale New South Wales 2351 Australia
| | - Ross M. Thompson
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Keith B. Gido
- Division of Biology; Kansas State University; Manhattan KS U.S.A
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14
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Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M. Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Mol Ecol Resour 2017; 18:306-318. [PMID: 29024429 DOI: 10.1111/1755-0998.12725] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 12/18/2022]
Abstract
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Asker D Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Hoppe
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yun Feng
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
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15
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King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MWW, Hazen TC, Arkin AP, Elias DA. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2879-2889. [PMID: 28112946 DOI: 10.1021/acs.est.6b04751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.
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Affiliation(s)
- Andrew J King
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Sarah P Preheim
- Department of Environmental Health and Enginering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Kathryn L Bailey
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Michael S Robeson
- Fish, Wildlife and Conservation Biology, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Taniya Roy Chowdhury
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Bryan R Crable
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Richard A Hurt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Tonia Mehlhorn
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Kenneth A Lowe
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Tommy J Phelps
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Anthony V Palumbo
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Craig C Brandt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Ping Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - David B Watson
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Matthew W Fields
- Department of Microbiology & Immunology, Montana State University , Bozeman, Montana 59717, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Eric J Alm
- Civil and Environmental Engineering and Biological Engineering, Massachusets Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
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16
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Puzon GJ, Wylie JT, Walsh T, Braun K, Morgan MJ. Comparison of biofilm ecology supporting growth of individual Naegleria species in a drinking water distribution system. FEMS Microbiol Ecol 2017; 93:3044201. [DOI: 10.1093/femsec/fix017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/20/2017] [Indexed: 01/06/2023] Open
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17
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Bondarenko NI, Bondarenko AS, Smirnov AV. Lineage-Specific and Highly Derived Gene Sequences Among Amoebozoa, Revealed by the Comparative Analysis of Transcriptomes from Twelve Amoebozoan Species. J Eukaryot Microbiol 2017; 64:622-631. [PMID: 28166371 DOI: 10.1111/jeu.12397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 11/28/2022]
Abstract
Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge of the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages. A potential way to resolve this problem is the usage of DNA barcodes based on genes, which are unique or highly derived in this group of organisms. In the present study, we attempted to find such genes and gene families with a low level of paralogy, potentially appropriate as Amoebozoa-specific DNA barcodes. For this we re-assembled transcriptomes of 12 amoebozoan species available from the public databases and performed gene annotation and identification of orthologous genes. In our analysis Amoebozoa-specific and highly derived sequences formed 53,182 clusters of orthologs, containing from 2 to 299 proteins each. Some of these genes may be a potential target for DNA barcoding of Amoebozoa.
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Affiliation(s)
- Natalya I Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
| | - Anton S Bondarenko
- Faculty of Physics, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Alexey V Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
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18
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Colloff M, Lavorel S, Wise RM, Dunlop M, Overton IC, Williams KJ. Adaptation services of floodplains and wetlands under transformational climate change. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:1003-1017. [PMID: 27509744 DOI: 10.1890/15-0848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Adaptation services are the ecosystem processes and services that benefit people by increasing their ability to adapt to change. Benefits may accrue from existing but newly used services where ecosystems persist or from novel services supplied following ecosystem transformation. Ecosystem properties that enable persistence or transformation are important adaptation services because they support future options. The adaptation services approach can be applied to decisions on trade-offs between currently valued services and benefits from maintaining future options. For example, ecosystem functions and services of floodplains depend on river flows. In those regions of the world where climate change projections are for hotter, drier conditions, floods will be less frequent and floodplains will either persist, though with modified structure and function, or transform to terrestrial (flood-independent) ecosystems. Many currently valued ecosystem services will reduce in supply or become unavailable, but new options are provided by adaptation services. We present a case study from the Murray-Darling Basin, Australia, for operationalizing the adaptation services concept for floodplains and wetlands. We found large changes in flow and flood regimes are likely under a scenario of +1.6°C by 2030, even with additional water restored to rivers under the proposed Murray-Darling Basin Plan. We predict major changes to floodplain ecosystems, including contraction of riparian forests and woodlands and expansion of terrestrial, drought-tolerant vegetation communities. Examples of adaptation services under this scenario include substitution of irrigated agriculture with dryland cropping and floodplain grazing; mitigation of damage from rarer, extreme floods; and increased tourism, recreational, and cultural values derived from fewer, smaller wetlands that can be maintained with environmental flows. Management for adaptation services will require decisions on where intervention can enable ecosystem persistence and where transformation is inevitable. New ways of managing water that include consideration of the increasing importance of adaptation services requires major changes to decision-making that better account for landscape heterogeneity and large-scale change rather than attempting to maintain ecosystems in fixed states.
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19
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Jacquiod S, Stenbæk J, Santos SS, Winding A, Sørensen SJ, Priemé A. Metagenomes provide valuable comparative information on soil microeukaryotes. Res Microbiol 2016; 167:436-50. [DOI: 10.1016/j.resmic.2016.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/16/2016] [Accepted: 03/20/2016] [Indexed: 02/02/2023]
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20
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Morgan MJ, Halstrom S, Wylie JT, Walsh T, Kaksonen AH, Sutton D, Braun K, Puzon GJ. Characterization of a Drinking Water Distribution Pipeline Terminally Colonized by Naegleria fowleri. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2890-2898. [PMID: 26853055 DOI: 10.1021/acs.est.5b05657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Free-living amoebae, such as Naegleria fowleri, Acanthamoeba spp., and Vermamoeba spp., have been identified as organisms of concern due to their role as hosts for pathogenic bacteria and as agents of human disease. In particular, N. fowleri is known to cause the disease primary amoebic meningoencephalitis (PAM) and can be found in drinking water systems in many countries. Understanding the temporal dynamics in relation to environmental and biological factors is vital for developing management tools for mitigating the risks of PAM. Characterizing drinking water systems in Western Australia with a combination of physical, chemical and biological measurements over the course of a year showed a close association of N. fowleri with free chlorine and distance from treatment over the course of a year. This information can be used to help design optimal management strategies for the control of N. fowleri in drinking-water-distribution systems.
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Affiliation(s)
- Matthew J Morgan
- CSIRO Land and Water , Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Samuel Halstrom
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Jason T Wylie
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water , Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Anna H Kaksonen
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - David Sutton
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Kalan Braun
- Water Corporation of Western Australia , 629 Newcastle Street, Leederville, Western Australia 6007, Australia
| | - Geoffrey J Puzon
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
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21
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Coissac E, Hollingsworth PM, Lavergne S, Taberlet P. From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol 2016; 25:1423-8. [DOI: 10.1111/mec.13549] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Coissac
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | | | - Sébastien Lavergne
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | - Pierre Taberlet
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
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22
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Tedersoo L, Bahram M, Cajthaml T, Põlme S, Hiiesalu I, Anslan S, Harend H, Buegger F, Pritsch K, Koricheva J, Abarenkov K. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. THE ISME JOURNAL 2016; 10:346-62. [PMID: 26172210 PMCID: PMC4737927 DOI: 10.1038/ismej.2015.116] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022]
Abstract
Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomáš Cajthaml
- Institute of Microbiology AS CR, Prague, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Sergei Põlme
- Natural History Museum, University of Tartu, Tartu, Estonia
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Helery Harend
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | | | - Julia Koricheva
- School of Biological Sciences, Royal Holloway University of London, Surrey, UK
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23
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Fiore-Donno AM, Weinert J, Wubet T, Bonkowski M. Metacommunity analysis of amoeboid protists in grassland soils. Sci Rep 2016; 6:19068. [PMID: 26750872 PMCID: PMC4707496 DOI: 10.1038/srep19068] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
This study reveals the diversity and distribution of two major ubiquitous groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes (plasmodial slime-moulds) that are rarely, if ever, recovered in environmental sampling studies. We analyzed 150 grassland soil samples from three Biodiversity Exploratories study regions in Germany. We developed specific primers targeting the V2 variable region in the first part of the small subunit of the ribosomal RNA gene for high-throughput pyrotag sequencing. From ca. 1 million reads, applying very stringent filtering and clustering parameters to avoid overestimation of the diversity, we obtained 273 acanthamoebal and 338 myxomycete operational taxonomic units (OTUs, 96% similarity threshold). This number is consistent with the genetic diversity known in the two investigated lineages, but unequalled to date by any environmental sampling study. Only very few OTUs were identical to already known sequences. Strikingly different OTUs assemblages were found between the three German regions (PerMANOVA p.value = 0.001) and even between sites of the same region (multiple-site Simpson-based similarity indices <0.4), showing steep biogeographical gradients.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Institute of Zoology, Department of Terrestrial Ecology, University of Cologne, Cologne, Germany
| | - Jan Weinert
- Institute of Zoology, Department of Terrestrial Ecology, University of Cologne, Cologne, Germany
| | - Tesfaye Wubet
- UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Michael Bonkowski
- Institute of Zoology, Department of Terrestrial Ecology, University of Cologne, Cologne, Germany
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Molecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding. Methods Mol Biol 2016; 1399:125-40. [PMID: 26791500 DOI: 10.1007/978-1-4939-3369-3_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
While until recently the application of high-throughput sequencing approaches has mostly been restricted to bacteria and fungi, these methods have now also become available to less often studied (eukaryotic) groups, such as fauna and protists. Such approaches allow routine diversity screening for large numbers of samples via DNA metabarcoding. Given the enormous taxonomic diversity within the eukaryote tree of life, metabarcoding approaches targeting a single specific DNA region do not allow to discriminate members of all eukaryote clades at high taxonomic resolution. Here, we report on protocols that enable studying the diversity of soil eukaryotes and, at high taxonomic resolution, of individual faunal and protist groups therein using a tiered approach: first, the use of a general eukaryotic primer set targeting a wide range of eukaryotes provides a rough impression on the entire diversity of protists and faunal groups. Second, more focused approaches enable deciphering subsets of soil eukaryotes in higher taxonomic detail. We provide primers and protocols for two examples: soil microarthropods and cercozoan protists.
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Geisen S, Tveit AT, Clark IM, Richter A, Svenning MM, Bonkowski M, Urich T. Metatranscriptomic census of active protists in soils. THE ISME JOURNAL 2015; 9:2178-90. [PMID: 25822483 PMCID: PMC4579471 DOI: 10.1038/ismej.2015.30] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/08/2022]
Abstract
The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
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Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
- Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), Wageningen, The Netherlands
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ian M Clark
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Andreas Richter
- Department of Microbiology and Ecosystem Sciences, University of Vienna, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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Chariton AA, Stephenson S, Morgan MJ, Steven ADL, Colloff MJ, Court LN, Hardy CM. Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 203:165-174. [PMID: 25909325 DOI: 10.1016/j.envpol.2015.03.047] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 05/10/2023]
Abstract
DNA-derived measurements of biological composition have the potential to produce data covering all of life, and provide a tantalizing proposition for researchers and managers. We used metabarcoding to compare benthic eukaryote composition from five estuaries of varying condition. In contrast to traditional studies, we found biotic richness was greatest in the most disturbed estuary, with this being due to the large volume of extraneous material (i.e. run-off from aquaculture, agriculture and other catchment activities) being deposited in the system. In addition, we found strong correlations between composition and a number of environmental variables, including nutrients, pH and turbidity. A wide range of taxa responded to these environmental gradients, providing new insights into their sensitivities to natural and anthropogenic stressors. Metabarcoding has the capacity to bolster current monitoring techniques, enabling the decisions regarding ecological condition to be based on a more holistic view of biodiversity.
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Affiliation(s)
- Anthony A Chariton
- CSIRO Oceans and Atmosphere, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
| | - Sarah Stephenson
- CSIRO Oceans and Atmosphere, Locked Bag 2007, Kirrawee, NSW 2232, Australia
| | - Matthew J Morgan
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Andrew D L Steven
- CSIRO Oceans and Atmosphere, GPO Box 2583, Brisbane, QLD 4001, Australia
| | | | - Leon N Court
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT 2601, Australia
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Clarke LJ, Weyrich LS, Cooper A. Reintroduction of locally extinct vertebrates impacts arid soil fungal communities. Mol Ecol 2015; 24:3194-205. [DOI: 10.1111/mec.13229] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Laurence J. Clarke
- Australian Centre for Ancient DNA; University of Adelaide; Adelaide SA 5005 Australia
- Australian Antarctic Division; Channel Highway; Kingston Tas. 7050 Australia
- Antarctic Climate & Ecosystems Cooperative Research Centre; University of Tasmania; Private Bag 80 Hobart Tas. 7001 Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA; University of Adelaide; Adelaide SA 5005 Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA; University of Adelaide; Adelaide SA 5005 Australia
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Geisen S, Laros I, Vizcaíno A, Bonkowski M, de Groot GA. Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Mol Ecol 2015; 24:4556-69. [DOI: 10.1111/mec.13238] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/02/2023]
Affiliation(s)
- S. Geisen
- Department of Terrestrial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); PO Box 50 6700 AB Wageningen, the Netherlands
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str 47b, 50674 Cologne Germany
| | - I. Laros
- ALTERRA - Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - A. Vizcaíno
- AllGenetics, Ed. de Servicios Centrales de Investigación; Campus de Elviña s/n E-15071 A Coruña Spain
| | - M. Bonkowski
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str 47b, 50674 Cologne Germany
| | - G. A. de Groot
- ALTERRA - Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
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29
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Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E. obitools: a unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 2015; 16:176-82. [PMID: 25959493 DOI: 10.1111/1755-0998.12428] [Citation(s) in RCA: 452] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/05/2015] [Indexed: 11/27/2022]
Abstract
DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
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Affiliation(s)
- Frédéric Boyer
- Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France
| | - Céline Mercier
- Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France
| | - Aurélie Bonin
- Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France
| | - Yvan Le Bras
- GenOuest Core Facility, CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France
| | - Eric Coissac
- Laboratoire d'Écologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourrier, BP 53, 38041, Grenoble Cedex-9, France
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Shen C, Liang W, Shi Y, Lin X, Zhang H, Wu X, Xie G, Chain P, Grogan P, Chu H. Contrasting elevational diversity patterns between eukaryotic soil microbes and plants. Ecology 2014. [DOI: 10.1890/14-0310.1] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Porazinska DL, Morgan MJ, Gaspar JM, Court LN, Hardy CM, Hodda M. Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics. PHYTOPATHOLOGY 2014; 104:749-761. [PMID: 24915429 DOI: 10.1094/phyto-08-13-0236-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.
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Lentendu G, Wubet T, Chatzinotas A, Wilhelm C, Buscot F, Schlegel M. Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach. Mol Ecol 2014; 23:3341-55. [DOI: 10.1111/mec.12819] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Guillaume Lentendu
- Plant Physiology; Institute of Biology; University of Leipzig; Johannisallee 21-23 Leipzig 04103 Germany
- Molecular Evolution and Animal Systematics; Institute of Biology; University of Leipzig; Talstraße 33 Leipzig 04103 Germany
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology; UFZ - Helmholtz Centre for Environmental Research; Permoserstraße 15 Leipzig 04318 Germany
| | - Christian Wilhelm
- Plant Physiology; Institute of Biology; University of Leipzig; Johannisallee 21-23 Leipzig 04103 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - François Buscot
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics; Institute of Biology; University of Leipzig; Talstraße 33 Leipzig 04103 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
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Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol 2014; 5:298. [PMID: 24995004 PMCID: PMC4063188 DOI: 10.3389/fmicb.2014.00298] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/30/2014] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.
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Affiliation(s)
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO, USA
| | - Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Jose C Clemente
- Biofrontiers Institute, University of Colorado Boulder, CO, USA
| | | | | | | | | | | | | | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago Chicago, IL, USA ; Institute of Genomic and Systems Biology, Argonne National Laboratory Argonne, IL, USA
| | - Rob Knight
- Biofrontiers Institute, University of Colorado Boulder, CO, USA ; Howard Hughes Medical Institute, University of Colorado Boulder, CO, USA
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35
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Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, Kitching R, Dolman PM, Woodcock P, Edwards FA, Larsen TH, Hsu WW, Benedick S, Hamer KC, Wilcove DS, Bruce C, Wang X, Levi T, Lott M, Emerson BC, Yu DW. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett 2013; 16:1245-57. [DOI: 10.1111/ele.12162] [Citation(s) in RCA: 414] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/11/2013] [Accepted: 07/01/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
| | - Louise Ashton
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
| | - Scott M. Pedley
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - David P. Edwards
- Woodrow Wilson School of Public and International Affairs Princeton University Princeton New Jersey 08544 USA
- Centre for Tropical Environmental and Sustainability Science (TESS) School of Marine and Tropical Biology James Cook University Cairns Queensland 4878 Australia
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544 USA
| | - Yong Tang
- Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Meng La Yunnan 666303 China
| | - Akihiro Nakamura
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
- Queensland Museum South Brisbane Queensland 4101 Australia
| | - Roger Kitching
- Environmental Futures Centre and Griffith School of Environment Griffith University Nathan Queensland 4111 Australia
| | - Paul M. Dolman
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Paul Woodcock
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - Felicity A. Edwards
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - Trond H. Larsen
- The Betty and Gordon Moore Center for Ecosystem Science and Economics Conservation International Arlington Virginia 22202 USA
| | - Wayne W. Hsu
- Department of Ecology Evolution, and Environmental Biology Columbia University New York City New York 10027 USA
| | - Suzan Benedick
- School of Sustainable Agriculture Universiti Malaysia Sabah Sandakan Sabah 9000 Malaysia
| | - Keith C. Hamer
- Institute of Integrative and Comparative Biology and Faculty of Biological Sciences University of Leeds Leeds West Yorkshire LS29JT UK
| | - David S. Wilcove
- Woodrow Wilson School of Public and International Affairs Princeton University Princeton New Jersey 08544 USA
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey 08544 USA
| | - Catharine Bruce
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
| | - Taal Levi
- Cary Institute of Ecosystem Studies Millbrook New York 12545 USA
- Department of Biology University of Florida Gainesville Florida 32611 USA
| | - Martin Lott
- School of Computing Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group IPNA‐CSIC Tenerife Canary Islands 38206 Spain
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
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