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Thakur R, Collens A, Greco M, Sleith RS, Grattepanche JD, Katz LA. Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses. J Eukaryot Microbiol 2022; 69:e12913. [PMID: 35332619 DOI: 10.1111/jeu.12913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Foraminifera include diverse shell-building lineages found in a wide array of aquatic habitats from the deep-sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera-specific primers that target the hypervariable regions of the foraminifera SSU-rRNA gene (~250-300bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority are undetermined taxa that have no closely-matching sequences in the database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single-chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa-like forms. Our pilot study provides the community with an additional set of newly designed and taxon-specific primers to elucidate foraminiferal diversity across different habitats.
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Affiliation(s)
- Rabindra Thakur
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Adena Collens
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Mattia Greco
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Temple University, Department of Biology, Philadelphia, Pennsylvania, USA
| | - Robin S Sleith
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Jean-David Grattepanche
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Laura A Katz
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
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2
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Fawley MW, Fawley KP, Cahoon AB. Finding needles in a haystack-Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbcL gene using lineage-directed primers. JOURNAL OF PHYCOLOGY 2021; 57:1636-1647. [PMID: 34218435 PMCID: PMC8530920 DOI: 10.1111/jpy.13196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 05/02/2023]
Abstract
Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastid rbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184 rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA-based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species-level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.
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Affiliation(s)
- Marvin W. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - Karen P. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - A. Bruce Cahoon
- Department of Natural Sciences, University of Virginia’s College at Wise, Wise, VA 24293, USA
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3
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Velasco-González I, Sanchez-Jimenez A, Singer D, Murciano A, Díez-Hermano S, Lara E, Martín-Cereceda M. Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes. MICROBIAL ECOLOGY 2020; 79:882-897. [PMID: 31796996 DOI: 10.1007/s00248-019-01463-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.
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Affiliation(s)
- Ismael Velasco-González
- Departamento de Genética, Fisiología y Microbiología. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid (UCM), C/ José Antonio Novais 12, 28040, Madrid, Spain
| | - Abel Sanchez-Jimenez
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Antonio Murciano
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - Sergio Díez-Hermano
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico, CSIC Plaza de Murillo 2, 28014, Madrid, Spain
| | - Mercedes Martín-Cereceda
- Departamento de Genética, Fisiología y Microbiología. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid (UCM), C/ José Antonio Novais 12, 28040, Madrid, Spain.
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4
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Forster D, Lentendu G, Filker S, Dubois E, Wilding TA, Stoeck T. Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants. Environ Microbiol 2019; 21:4109-4124. [PMID: 31361938 DOI: 10.1111/1462-2920.14764] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
Abstract
Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high-throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina-sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second-level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM-SSNs, NSC numbers decreased from 7.9-fold overestimation without abundance filter, to 4.5-fold overestimation when an abundance filter was applied. For the DADA2-SSN approach, NSC numbers decreased from 3.5-fold to 3-fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2-SSNs and SWARM-SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.
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Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Elyssa Dubois
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, UK
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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5
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Santamaria M, Fosso B, Licciulli F, Balech B, Larini I, Grillo G, De Caro G, Liuni S, Pesole G. ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. Nucleic Acids Res 2019; 46:D127-D132. [PMID: 29036529 PMCID: PMC5753230 DOI: 10.1093/nar/gkx855] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/18/2017] [Indexed: 01/21/2023] Open
Abstract
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.
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Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Flavio Licciulli
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Ilaria Larini
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari 'A. Moro', Bari 70126, Italy
| | - Giorgio Grillo
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Giorgio De Caro
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Sabino Liuni
- Institute of Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari 'A. Moro', Bari 70126, Italy
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6
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Pasulka A, Hu SK, Countway PD, Coyne KJ, Cary SC, Heidelberg KB, Caron DA. SSU-rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent. J Eukaryot Microbiol 2019; 66:637-653. [PMID: 30620427 DOI: 10.1111/jeu.12711] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/09/2018] [Accepted: 12/16/2018] [Indexed: 12/21/2022]
Abstract
Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep-sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high-throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates (especially dinoflagellates and ciliates) and cercozoans. OTU richness and community structure differed among sediment habitats (e.g. different mat types and cold sediments away from mats). Additionally, full-length 18S rRNA genes amplified and cloned from single cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity.
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Affiliation(s)
- Alexis Pasulka
- Biological Sciences Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, USA
| | - Sarah K Hu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 301 Los Angeles, Los Angeles, California, USA
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, Maine, USA
| | - Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, Lewes, Delaware, USA
| | - Stephen C Cary
- Department of Biological Sciences, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 301 Los Angeles, Los Angeles, California, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 301 Los Angeles, Los Angeles, California, USA
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7
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Tekle YI, Wood FC. A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes. BMC Evol Biol 2018; 18:170. [PMID: 30445905 PMCID: PMC6240226 DOI: 10.1186/s12862-018-1283-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories. Conclusion Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1283-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fiona C Wood
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
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8
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Cahoon AB, Huffman AG, Krager MM, Crowell RM. A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.26939] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The purpose of our study was to survey the freshwater planktonic protists within an inland natural preserve in the Ridge and Valley physiographic province of the Appalachian Region using metabarcoding. Microbial eukaryotes are essential primary producers and predators in small freshwater ecosystems, yet they are often overlooked due to the difficulty of identification. This has been remedied, in part, by the cost reduction of high throughput DNA sequencing and the growth of barcode databases, making the identification and analysis of microorganisms by way of metabarcoding surveys in complex ecosystems increasingly feasible. Water samples were collected from five sites at the Natural Tunnel State Park in Scott County, VA (USA), representing three common bodies of water found in this region. Samples were initially collected during a Bioblitz event in April 2016 and then seven and fourteen weeks afterwards. Metabarcode analysis of the 23S and 18S genes identified 3663 OTUs representing 213 family level and 332 genus level taxa. This study provides an initial barcode census within a region that has a reputation as a temperate biodiversity “hotspot”. The overall protist diversity was comparably high to other temperate systems, but not unusually high; the microalgal diversity, however, was higher than that reported for other temperate regions. The three types of water bodies had their own distinctive protist biomes despite close proximity.
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9
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Birrer SC, Dafforn KA, Simpson SL, Kelaher BP, Potts J, Scanes P, Johnston EL. Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1383-1394. [PMID: 29801231 DOI: 10.1016/j.scitotenv.2018.05.065] [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: 02/21/2018] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.
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Affiliation(s)
- Simone C Birrer
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia.
| | - Katherine A Dafforn
- The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia; Department of Environmental Sciences, Macquarie University, North Ryde NSW 2109, Australia
| | | | - Brendan P Kelaher
- National Marine Science Centre and Centre for Coastal Biogeochemistry Research, Southern Cross University, Coffs Harbour 2450, NSW, Australia
| | - Jaimie Potts
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Peter Scanes
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Emma L Johnston
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia
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10
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Todman LC, Fraser FC, Corstanje R, Harris JA, Pawlett M, Ritz K, Whitmore AP. Evidence for functional state transitions in intensively-managed soil ecosystems. Sci Rep 2018; 8:11522. [PMID: 30068982 PMCID: PMC6070522 DOI: 10.1038/s41598-018-29925-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/17/2018] [Indexed: 11/16/2022] Open
Abstract
Soils are fundamental to terrestrial ecosystem functioning and food security, thus their resilience to disturbances is critical. Furthermore, they provide effective models of complex natural systems to explore resilience concepts over experimentally-tractable short timescales. We studied soils derived from experimental plots with different land-use histories of long-term grass, arable and fallow to determine whether regimes of extreme drying and re-wetting would tip the systems into alternative stable states, contingent on their historical management. Prior to disturbance, grass and arable soils produced similar respiration responses when processing an introduced complex carbon substrate. A distinct respiration response from fallow soil here indicated a different prior functional state. Initial dry:wet disturbances reduced the respiration in all soils, suggesting that the microbial community was perturbed such that its function was impaired. After 12 drying and rewetting cycles, despite the extreme disturbance regime, soil from the grass plots, and those that had recently been grass, adapted and returned to their prior functional state. Arable soils were less resilient and shifted towards a functional state more similar to that of the fallow soil. Hence repeated stresses can apparently induce persistent shifts in functional states in soils, which are influenced by management history.
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Affiliation(s)
- L C Todman
- Rothamsted Research, Harpenden, AL5 2JQ, UK.
| | - F C Fraser
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - R Corstanje
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - J A Harris
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - M Pawlett
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
| | - K Ritz
- Cranfield University, Cranfield, Bedford, MK43 0AL, UK
- The University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
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11
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Grattepanche J, Walker LM, Ott BM, Paim Pinto DL, Delwiche CF, Lane CE, Katz LA. Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data. Bioessays 2018; 40:e1700198. [DOI: 10.1002/bies.201700198] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
| | - Laura M. Walker
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
| | - Brittany M. Ott
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | | | - Charles F. Delwiche
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | - Christopher E. Lane
- Department of Biological SciencesUniversity of Rhode IslandKingstonRI 02881USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
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12
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Eukaryotic microbial richness increases with latitude and decreasing temperature in the Pacific Subarctic domain in late winter. Polar Biol 2017. [DOI: 10.1007/s00300-017-2131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Santoferrara LF, McManus GB. Integrating dimensions of biodiversity in choreotrichs and oligotrichs of marine plankton. Eur J Protistol 2017; 61:323-330. [DOI: 10.1016/j.ejop.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 01/01/2023]
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14
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Dean SL, Billingsley Tobias T, Phippen WB, Clayton AW, Gruver J, Porras-Alfaro A. A study of Glycine max (soybean) fungal communities under different agricultural practices. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Ainsworth TD, Fordyce AJ, Camp EF. The Other Microeukaryotes of the Coral Reef Microbiome. Trends Microbiol 2017; 25:980-991. [PMID: 28720387 DOI: 10.1016/j.tim.2017.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 12/21/2022]
Abstract
In marine ecosystems microbial communities are critical to ocean function, global primary productivity, and biogeochemical cycles. Both prokaryotic and eukaryotic microbes are essential symbionts and mutualists, nonpathogenic invaders, primary pathogens, have been linked to disease emergence, and can underpin broader ecosystem changes. However, in the effort to determine coral-microbial interactions, the structure and function of the eukaryotic microbes of the microbiome have been studied less. Eukaryotic microbes are important members of the microbiome, constitute entire kingdoms of life, and make important contributions to ecosystem function. Here, we outline the roles of eukaryotic microbes in marine systems and their contribution to ecosystem change, and discuss the microeukaryotic microbiome of corals and coral reefs.
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Affiliation(s)
- T D Ainsworth
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4810, QLD, Australia.
| | - A J Fordyce
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4810, QLD, Australia
| | - E F Camp
- Climate Change Cluster, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
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Debroas D, Domaizon I, Humbert JF, Jardillier L, Lepère C, Oudart A, Taïb N. Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data. FEMS Microbiol Ecol 2017; 93:3059202. [DOI: 10.1093/femsec/fix023] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/28/2017] [Indexed: 12/21/2022] Open
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Bhute SS, Suryavanshi MV, Joshi SM, Yajnik CS, Shouche YS, Ghaskadbi SS. Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes. Front Microbiol 2017; 8:214. [PMID: 28261173 PMCID: PMC5306211 DOI: 10.3389/fmicb.2017.00214] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/30/2017] [Indexed: 12/11/2022] Open
Abstract
Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of eubacteria in response to the disease. PERMANOVA test indicated that the eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes, microbial dysbiosis may not be just limited to eubacteria. Due to the inter-linked metabolic interactions among the eubacteria, archaea and eukarya in the gut, it may extend into other two domains leading to trans-domain dysbiosis in microbiota. Our results thus contribute to and expand the identification of biomarkers in diabetes.
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Affiliation(s)
- Shrikant S Bhute
- Department of Zoology, Savitribai Phule Pune University Pune, India
| | | | - Suyog M Joshi
- Diabetes Unit, KEM Hospital and Research Centre Pune, India
| | | | - Yogesh S Shouche
- Microbial Culture Collection-National Centre for Cell Science Pune, India
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Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf. PLoS One 2016; 11:e0167659. [PMID: 27936137 PMCID: PMC5147948 DOI: 10.1371/journal.pone.0167659] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/17/2016] [Indexed: 11/29/2022] Open
Abstract
Although protists (microbial eukaryotes) provide an important link between bacteria and Metazoa in food webs, we do not yet have a clear understanding of the spatial scales on which protist diversity varies. Here, we use a combination of DNA fingerprinting (denaturant gradient gel electrophoresis or DGGE) and high-throughput sequencing (HTS) to assess the ciliate community in the class Spirotrichea at varying scales of 1–3 km sampled in three locations separated by at least 25 km—offshore, midshelf and inshore—along the New England shelf. Analyses of both abundant community (DGGE) and the total community (HTS) members reveal that: 1) ciliate communities are patchily distributed inshore (i.e. the middle station of a transect is distinct from its two neighboring stations), whereas communities are more homogeneous among samples within the midshelf and offshore stations; 2) a ciliate closely related to Pelagostrobilidium paraepacrum ‘blooms’ inshore and; 3) environmental factors may differentially impact the distributions of individual ciliates (i.e. OTUs) rather than the community as a whole as OTUs tend to show distinct biogeographies (e.g. some OTUs are restricted to the offshore locations, some to the surface, etc.). Together, these data show the complexity underlying the spatial distributions of marine protists, and suggest that biogeography may be a property of ciliate species rather than communities.
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Daïnou K, Blanc-Jolivet C, Degen B, Kimani P, Ndiade-Bourobou D, Donkpegan ASL, Tosso F, Kaymak E, Bourland N, Doucet JL, Hardy OJ. Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol Biol 2016; 16:259. [PMID: 27903256 PMCID: PMC5131513 DOI: 10.1186/s12862-016-0831-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium. .,Université d'Agriculture de Kétou, BP 43, Kétou, Benin.
| | - Céline Blanc-Jolivet
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Bernd Degen
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Priscilla Kimani
- Kenya Forestry Research Institute, Biotechnology Section, P. O. Box 20412-00200, Nairobi, Kenya
| | | | - Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Esra Kaymak
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
| | - Nils Bourland
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
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Grattepanche J, Santoferrara LF, McManus GB, Katz LA. Unexpected biodiversity of ciliates in marine samples from below the photic zone. Mol Ecol 2016; 25:3987-4000. [DOI: 10.1111/mec.13745] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - George B. McManus
- Department of Marine Sciences University of Connecticut Groton CT 06340 USA
| | - Laura A. Katz
- Department of Biological Sciences Smith College Northampton MA 01063 USA
- Program in Organismic and Evolutionary Biology University of Massachusetts Amherst MA 01003 USA
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21
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Protist metabarcoding and environmental biomonitoring: Time for change. Eur J Protistol 2016; 55:12-25. [DOI: 10.1016/j.ejop.2016.02.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/29/2016] [Accepted: 02/12/2016] [Indexed: 01/06/2023]
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Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem. Appl Environ Microbiol 2016; 82:2494-2505. [PMID: 26896141 DOI: 10.1128/aem.03965-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/02/2016] [Indexed: 02/01/2023] Open
Abstract
Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms.
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23
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Ghosh S, Chowdhury R, Bhattacharya P. Mixed consortia in bioprocesses: role of microbial interactions. Appl Microbiol Biotechnol 2016; 100:4283-95. [DOI: 10.1007/s00253-016-7448-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 12/22/2022]
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Santoferrara LF, Grattepanche JD, Katz LA, McManus GB. Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? ISME JOURNAL 2016; 10:1779-90. [PMID: 26849313 DOI: 10.1038/ismej.2015.224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/28/2015] [Accepted: 11/03/2015] [Indexed: 01/28/2023]
Abstract
Our knowledge on microbial biogeography depends on the way we define and study diversity. In contrast to most microbes, some protist lineages have conspicuous structures that allow comparisons of diversity concepts and measures-those based on molecules and those based on morphology. We analyzed a group of shell-bearing planktonic ciliates, the tintinnids, in a coast-to-ocean gradient using high-throughput sequencing and microscopy. First, we compared molecular operational taxonomic units (OTUs) and morphospecies in terms of assemblage composition, distribution and relationships with the environment. OTUs revealed potentially novel and rare taxa, while morphospecies showed clearer correlations with environmental factors, and both approaches coincided in supporting a coastal versus oceanic pattern. Second, we explored which processes influence assembly across the environmental gradient examined. Assemblage fluctuations were associated with significant distance-decay and changes in morphospecies size and prey proxies, thus suggesting niche partitioning as a key structuring mechanism. Our conclusion is that molecules and morphologies generally agreed, but they provided complementary data, the first revealing hidden diversity, and the latter making better connections between distribution patterns and ecological processes. This highlights the importance of linking genotypes and phenotypes (using multidisciplinary analyses and/or reliable databases of barcoded species), to understand the diversity, biogeography and ecological roles of microbes.
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Affiliation(s)
| | | | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, USA.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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25
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Hu SK, Liu Z, Lie AAY, Countway PD, Kim DY, Jones AC, Gast RJ, Cary SC, Sherr EB, Sherr BF, Caron DA. Estimating Protistan Diversity Using High-Throughput Sequencing. J Eukaryot Microbiol 2015; 62:688-93. [PMID: 25851049 DOI: 10.1111/jeu.12217] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 11/28/2022]
Abstract
Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full-length sequences. A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full-length 18S rRNA gene sequences. Present high-throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences.
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Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Alle A Y Lie
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Diane Y Kim
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Adriane C Jones
- Mount St. Mary's College, Los Angeles, California, 90049, USA
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - S Craig Cary
- Environmental Research Institute, School of Science, University of Waikato, Hamilton, 3240, New Zealand.,College of Earth and Ocean Science, University of Delaware, Newark, Delaware, 19716, USA
| | - Evelyn B Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Barry F Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
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Lahr DJG, Laughinghouse HD, Oliverio AM, Gao F, Katz LA. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. Bioessays 2014; 36:950-9. [PMID: 25156897 DOI: 10.1002/bies.201400056] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, University of Sao Paulo, Sao Paulo, Brazil
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